SMO

UniProt ID: Q99835
Organism: Homo sapiens
Review Status: COMPLETE
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Gene Description

SMO (Smoothened) is a 787-amino-acid, seven-pass class-F G protein-coupled receptor and the obligate signal-transducing membrane component of vertebrate Hedgehog signaling. In the pathway-off state, PTCH1 or PTCH2 restricts SMO access to activating sterols. Hedgehog binding to Patched relieves this inhibition, allowing cholesterol and oxysterols to bind SMO's extracellular cysteine-rich domain and transmembrane sterol-binding sites, stabilize an active conformation, and promote accumulation of SMO in the primary-cilium membrane. Active SMO can couple to heterotrimeric Gi, lowering cAMP, and also directly binds and inhibits the catalytic subunit of protein kinase A through a C-terminal pseudosubstrate/PKI motif. These mechanisms prevent inhibitory phosphorylation and processing of GLI transcription factors and permit GLI-dependent transcription. SMO therefore functions principally at the plasma membrane and the membrane of non-motile primary cilia, with context-dependent roles in embryonic patterning, organogenesis, tissue homeostasis, and cell proliferation. Germline biallelic loss-of-function variants cause pleiotropic developmental anomalies through impaired Hedgehog signaling, whereas activating somatic or mosaic variants drive tumors and Curry-Jones syndrome.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005886 plasma membrane
IBA
GO_REF:0000033 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The plasma membrane annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
Cell membrane
GO:0005929 cilium
IBA
GO_REF:0000033 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
Cell projection, cilium membrane
GO:0007224 smoothened signaling pathway
IBA
GO_REF:0000033 		ACCEPT
Summary: SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This phylogenetic inference is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
G protein-coupled receptor, which transduces the smoothened signaling pathway
GO:0007417 central nervous system development
IBA
GO_REF:0000033 		KEEP AS NON CORE
Summary: The central nervous system development annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The phylogenetic inference (GO_REF:0000033) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0007389 pattern specification process
IBA
GO_REF:0000033 		KEEP AS NON CORE
Summary: The pattern specification process annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The phylogenetic inference (GO_REF:0000033) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0030425 dendrite
IBA
GO_REF:0000033 		KEEP AS NON CORE
Summary: The dendrite annotation is compatible with a context-specific localization, trafficking state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
Reason: Retained as non-core on the basis of phylogenetic inference (GO_REF:0000033); it is secondary to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
GO:0071679 commissural neuron axon guidance
IBA
GO_REF:0000033 		KEEP AS NON CORE
Summary: The commissural neuron axon guidance annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The phylogenetic inference (GO_REF:0000033) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0005113 patched binding
IBA
GO_REF:0000033 		KEEP AS NON CORE
Summary: Patched proteins negatively regulate SMO and older biochemical experiments reported PTCH-SMO complexes. Current mechanistic work emphasizes control of SMO sterol access rather than a required stable receptor complex.
Reason: Retained as non-core because the physical association is reported by PMID:9811851 and supported phylogenetically, but patched binding is not the principal molecular activity of SMO.
GO:0004888 transmembrane signaling receptor activity
IEA
GO_REF:0000002 		MODIFY
Summary: The transmembrane signaling receptor activity annotation is directionally correct but too broad to represent SMO's established function. SMO is a sterol-regulated class-F GPCR that transduces the smoothened pathway at plasma and ciliary membranes.
Reason: Modify to the more informative G protein-coupled receptor activity (GO:0004930). The replacement preserves the source inference (GO_REF:0000002) while matching the experimentally established specificity of SMO.
GO:0005886 plasma membrane
IEA
GO_REF:0000120 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The plasma membrane annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
GO:0007166 cell surface receptor signaling pathway
IEA
GO_REF:0000002 		MODIFY
Summary: The cell surface receptor signaling pathway annotation is directionally correct but too broad to represent SMO's established function. SMO is a sterol-regulated class-F GPCR that transduces the smoothened pathway at plasma and ciliary membranes.
Reason: Modify to the more informative smoothened signaling pathway (GO:0007224). The replacement preserves the source inference (GO_REF:0000002) while matching the experimentally established specificity of SMO.
Proposed replacements: smoothened signaling pathway
GO:0009888 tissue development
IEA
GO_REF:0000117 		MARK AS OVER ANNOTATED
Summary: The tissue development phenotype can occur downstream of altered SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear to be a direct activity of SMO.
Reason: Marked as over-annotated. The source (GO_REF:0000117; electronic inference) supports pathway perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling, and PKA-inhibitory functions.
GO:0016020 membrane
IEA
GO_REF:0000002 		MODIFY
Summary: The membrane annotation is directionally correct but too broad to represent SMO's established function. SMO is a sterol-regulated class-F GPCR that transduces the smoothened pathway at plasma and ciliary membranes.
Reason: Modify to the more informative plasma membrane (GO:0005886) and ciliary membrane (GO:0060170). The replacement preserves the source inference (GO_REF:0000002) while matching the experimentally established specificity of SMO.
GO:0060170 ciliary membrane
IEA
GO_REF:0000044 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The ciliary membrane annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
GO:0120025 plasma membrane bounded cell projection
IEA
GO_REF:0000117 		MODIFY
Summary: The plasma membrane bounded cell projection annotation is directionally correct but too broad to represent SMO's established function. SMO is a sterol-regulated class-F GPCR that transduces the smoothened pathway at plasma and ciliary membranes.
Reason: Modify to the more informative cilium (GO:0005929). The replacement preserves the source inference (GO_REF:0000117) while matching the experimentally established specificity of SMO.
Proposed replacements: cilium
GO:0001947 heart looping
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: The heart looping annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0003140 determination of left/right asymmetry in lateral mesoderm
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: The determination of left/right asymmetry in lateral mesoderm annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0004930 G protein-coupled receptor activity
IEA
GO_REF:0000107 		ACCEPT
Summary: The G protein-coupled receptor activity annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this electronic inference is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000107) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
G protein-coupled receptor, which transduces the smoothened signaling pathway
GO:0005929 cilium
IEA
GO_REF:0000107 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
Cell projection, cilium membrane
GO:0007193 adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
IEA
GO_REF:0000107 		ACCEPT
Summary: SMO is the membrane transducer of the adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This electronic inference is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
G protein-coupled receptor, which transduces the smoothened signaling pathway
GO:0007224 smoothened signaling pathway
IEA
GO_REF:0000107 		ACCEPT
Summary: SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This electronic inference is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
G protein-coupled receptor, which transduces the smoothened signaling pathway
GO:0007371 ventral midline determination
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: The ventral midline determination annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0007494 midgut development
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: The midgut development annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0008142 oxysterol binding
IEA
GO_REF:0000107 		ACCEPT
Summary: The oxysterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this electronic inference is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000107) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
In addition to cholesterol, SMO is also activated by various oxysterols
GO:0015485 cholesterol binding
IEA
GO_REF:0000107 		ACCEPT
Summary: The cholesterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this electronic inference is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000107) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
G protein-coupled receptor, which transduces the smoothened signaling pathway
GO:0021513 spinal cord dorsal/ventral patterning
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: The spinal cord dorsal/ventral patterning annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0034236 protein kinase A catalytic subunit binding
IEA
GO_REF:0000107 		ACCEPT
Summary: The protein kinase A catalytic subunit binding annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this electronic inference is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000107) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
Interacts (via PKI motif) with protein kinase A catalytic subunit PRKACA
GO:0040018 positive regulation of multicellular organism growth
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: The positive regulation of multicellular organism growth phenotype can occur downstream of altered SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear to be a direct activity of SMO.
Reason: Marked as over-annotated. The source (GO_REF:0000107; electronic inference) supports pathway perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling, and PKA-inhibitory functions.
GO:0045880 positive regulation of smoothened signaling pathway
IEA
GO_REF:0000107 		ACCEPT
Summary: SMO is the membrane transducer of the positive regulation of smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This electronic inference is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
G protein-coupled receptor, which transduces the smoothened signaling pathway
GO:0045892 negative regulation of DNA-templated transcription
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: The negative regulation of DNA-templated transcription phenotype can occur downstream of altered SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear to be a direct activity of SMO.
Reason: Marked as over-annotated. The source (GO_REF:0000107; electronic inference) supports pathway perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling, and PKA-inhibitory functions.
GO:0045893 positive regulation of DNA-templated transcription
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: The positive regulation of DNA-templated transcription phenotype can occur downstream of altered SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear to be a direct activity of SMO.
Reason: Marked as over-annotated. The source (GO_REF:0000107; electronic inference) supports pathway perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling, and PKA-inhibitory functions.
GO:0046622 positive regulation of organ growth
IEA
GO_REF:0000107 		MARK AS OVER ANNOTATED
Summary: The positive regulation of organ growth phenotype can occur downstream of altered SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear to be a direct activity of SMO.
Reason: Marked as over-annotated. The source (GO_REF:0000107; electronic inference) supports pathway perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling, and PKA-inhibitory functions.
GO:0048853 forebrain morphogenesis
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: The forebrain morphogenesis annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0061053 somite development
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: The somite development annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0071397 cellular response to cholesterol
IEA
GO_REF:0000107 		ACCEPT
Summary: SMO is the membrane transducer of the cellular response to cholesterol; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This electronic inference is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
G protein-coupled receptor, which transduces the smoothened signaling pathway
GO:0072285 mesenchymal to epithelial transition involved in metanephric renal vesicle formation
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: The mesenchymal to epithelial transition involved in metanephric renal vesicle formation annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0090190 positive regulation of branching involved in ureteric bud morphogenesis
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: The positive regulation of branching involved in ureteric bud morphogenesis annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0098804 non-motile cilium membrane
IEA
GO_REF:0000107 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The non-motile cilium membrane annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
Cell projection, cilium membrane
GO:0140311 protein sequestering activity
IEA
GO_REF:0000107 		ACCEPT
Summary: The protein sequestering activity annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this electronic inference is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000107) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
Interacts (via PKI motif) with protein kinase A catalytic subunit PRKACA
GO:2000826 regulation of heart morphogenesis
IEA
GO_REF:0000107 		KEEP AS NON CORE
Summary: The regulation of heart morphogenesis annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0004930 G protein-coupled receptor activity
IDA
PMID:27437577
Structural basis of Smoothened regulation by its extracellul... 		ACCEPT
Summary: The G protein-coupled receptor activity annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (PMID:27437577) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
PMID:27437577
Unexpectedly, we find a cholesterol molecule bound to Smoothened in the CRD binding site.
GO:0004930 G protein-coupled receptor activity
IDA
PMID:31168089
Cryo-EM structure of oxysterol-bound human Smoothened couple... 		ACCEPT
Summary: The G protein-coupled receptor activity annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (PMID:31168089) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
PMID:31168089
The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F), transduces the Hedgehog signal
GO:0004930 G protein-coupled receptor activity
IDA
PMID:32929279
Sterols in an intramolecular channel of Smoothened mediate H... 		ACCEPT
Summary: The G protein-coupled receptor activity annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (PMID:32929279) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
PMID:32929279
Smoothened (SMO), a class Frizzled G protein-coupled receptor (class F GPCR), transduces the Hedgehog signal across the cell membrane.
GO:0007193 adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
IDA
PMID:32929279
Sterols in an intramolecular channel of Smoothened mediate H... 		ACCEPT
Summary: SMO is the membrane transducer of the adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IDA experimental evidence is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
PMID:32929279
Smoothened (SMO), a class Frizzled G protein-coupled receptor (class F GPCR), transduces the Hedgehog signal across the cell membrane.
GO:0007224 smoothened signaling pathway
IDA
PMID:31168089
Cryo-EM structure of oxysterol-bound human Smoothened couple... 		ACCEPT
Summary: SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IDA experimental evidence is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
PMID:31168089
The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F), transduces the Hedgehog signal
GO:0007224 smoothened signaling pathway
IDA
PMID:32929279
Sterols in an intramolecular channel of Smoothened mediate H... 		ACCEPT
Summary: SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IDA experimental evidence is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
PMID:32929279
Smoothened (SMO), a class Frizzled G protein-coupled receptor (class F GPCR), transduces the Hedgehog signal across the cell membrane.
GO:0007224 smoothened signaling pathway
IDA
PMID:39138140
GRK2 kinases in the primary cilium initiate SMOOTHENED-PKA s... 		ACCEPT
Summary: SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IDA experimental evidence is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
PMID:39138140
GRK2 phosphorylation enables active SMO to bind PKA-C directly.
GO:0015485 cholesterol binding
IDA
PMID:27437577
Structural basis of Smoothened regulation by its extracellul... 		ACCEPT
Summary: The cholesterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (PMID:27437577) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
PMID:27437577
Unexpectedly, we find a cholesterol molecule bound to Smoothened in the CRD binding site.
GO:0015485 cholesterol binding
IDA
PMID:31168089
Cryo-EM structure of oxysterol-bound human Smoothened couple... 		ACCEPT
Summary: The cholesterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (PMID:31168089) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
PMID:31168089
The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F), transduces the Hedgehog signal
GO:0015485 cholesterol binding
IDA
PMID:32929279
Sterols in an intramolecular channel of Smoothened mediate H... 		ACCEPT
Summary: The cholesterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (PMID:32929279) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
PMID:32929279
Smoothened (SMO), a class Frizzled G protein-coupled receptor (class F GPCR), transduces the Hedgehog signal across the cell membrane.
GO:0140311 protein sequestering activity
IDA
PMID:39138140
GRK2 kinases in the primary cilium initiate SMOOTHENED-PKA s... 		ACCEPT
Summary: The protein sequestering activity annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (PMID:39138140) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
PMID:39138140
GRK2 phosphorylation enables active SMO to bind PKA-C directly.
GO:0007193 adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
IDA
PMID:31168089
Cryo-EM structure of oxysterol-bound human Smoothened couple... 		ACCEPT
Summary: SMO is the membrane transducer of the adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IDA experimental evidence is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
PMID:31168089
The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F), transduces the Hedgehog signal
GO:0098804 non-motile cilium membrane
IDA
PMID:31168089
Cryo-EM structure of oxysterol-bound human Smoothened couple... 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The non-motile cilium membrane annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
Supporting Evidence:
PMID:31168089
The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F), transduces the Hedgehog signal
GO:0140311 protein sequestering activity
IDA
PMID:36202993
A PKA inhibitor motif within SMOOTHENED controls Hedgehog si... 		ACCEPT
Summary: The protein sequestering activity annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (PMID:36202993) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
PMID:36202993
SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity.
GO:0098804 non-motile cilium membrane
IDA
PMID:22072986
A novel protein LZTFL1 regulates ciliary trafficking of the ... 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The non-motile cilium membrane annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
Supporting Evidence:
PMID:22072986
In control siRNA transfected cells, SMO localizes to the cilia in response to SMO agonist (SAG) but not in SAG-untreated cells
GO:0005929 cilium
IDA
GO_REF:0000052 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
GO:0005886 plasma membrane
ISS
GO_REF:0000024 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The plasma membrane annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
Cell membrane
GO:0045944 positive regulation of transcription by RNA polymerase II
ISS
GO_REF:0000024 		MARK AS OVER ANNOTATED
Summary: The positive regulation of transcription by RNA polymerase II phenotype can occur downstream of altered SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear to be a direct activity of SMO.
Reason: Marked as over-annotated. The source (GO_REF:0000024; curator-reviewed orthology transfer) supports pathway perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling, and PKA-inhibitory functions.
GO:0007224 smoothened signaling pathway
IDA
PMID:36202993
A PKA inhibitor motif within SMOOTHENED controls Hedgehog si... 		ACCEPT
Summary: SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IDA experimental evidence is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
PMID:36202993
SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity.
GO:0007224 smoothened signaling pathway
ISS
GO_REF:0000024 		ACCEPT
Summary: SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This curator-reviewed orthology transfer is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
G protein-coupled receptor, which transduces the smoothened signaling pathway
GO:0034236 protein kinase A catalytic subunit binding
ISS
GO_REF:0000024 		ACCEPT
Summary: The protein kinase A catalytic subunit binding annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this curator-reviewed orthology transfer is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000024) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
Interacts (via PKI motif) with protein kinase A catalytic subunit PRKACA
GO:0008142 oxysterol binding
ISS
GO_REF:0000024 		ACCEPT
Summary: The oxysterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and cellular studies; this curator-reviewed orthology transfer is concordant with that mechanism.
Reason: Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000024) is consistent with direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993, and PMID:39138140, as applicable to this activity.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
In addition to cholesterol, SMO is also activated by various oxysterols
GO:0005929 cilium
IDA
PMID:32413283
Bi-allelic Variations of SMO in Humans Cause a Broad Spectru... 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
Supporting Evidence:
PMID:32413283
Cells derived from affected individuals showed normal ciliogenesis but severely altered Hh-signal transduction as a result of either altered PC trafficking or abnormal activation of the pathway downstream of SMO.
GO:0007224 smoothened signaling pathway
IMP
PMID:32413283
Bi-allelic Variations of SMO in Humans Cause a Broad Spectru... 		ACCEPT
Summary: SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IMP experimental evidence is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
PMID:32413283
Cells derived from affected individuals showed normal ciliogenesis but severely altered Hh-signal transduction as a result of either altered PC trafficking or abnormal activation of the pathway downstream of SMO.
GO:0005929 cilium
IDA
PMID:27727273
Zfp423 Regulates Sonic Hedgehog Signaling via Primary Cilium... 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
Supporting Evidence:
PMID:27727273
loss of Zfp423 in these precursors leads to cell-intrinsic reduction in proliferation, loss of response to Shh, and primary cilia abnormalities that include diminished frequency of both Smoothened and IFT88 localization.
GO:0048745 smooth muscle tissue development
IEP
PMID:17850284
Immunohistochemical analysis of Sonic hedgehog signalling in... 		KEEP AS NON CORE
Summary: The smooth muscle tissue development annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The expression-pattern evidence (PMID:17850284) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
Supporting Evidence:
PMID:17850284
The expression patterns of the SHH-transducing proteins Patched (PTCH) and Smoothened (SMO) were consistent with long-range paracrine signalling associated with detrusor smooth muscle differentiation in the urogenital sinus.
GO:0010628 positive regulation of gene expression
IMP
PMID:21671467
miR-338-3p suppresses invasion of liver cancer cell by targe... 		MARK AS OVER ANNOTATED
Summary: The positive regulation of gene expression phenotype can occur downstream of altered SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear to be a direct activity of SMO.
Reason: Marked as over-annotated. The source (PMID:21671467; IMP experimental evidence) supports pathway perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling, and PKA-inhibitory functions.
Supporting Evidence:
PMID:21671467
small interfering RNA targeted SMO reversed the effects induced by blockade of miR-338-3p.
GO:0030335 positive regulation of cell migration
IMP
PMID:21671467
miR-338-3p suppresses invasion of liver cancer cell by targe... 		MARK AS OVER ANNOTATED
Summary: The positive regulation of cell migration phenotype can occur downstream of altered SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear to be a direct activity of SMO.
Reason: Marked as over-annotated. The source (PMID:21671467; IMP experimental evidence) supports pathway perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling, and PKA-inhibitory functions.
Supporting Evidence:
PMID:21671467
small interfering RNA targeted SMO reversed the effects induced by blockade of miR-338-3p.
GO:0005515 protein binding
IPI
PMID:21659505
Growth Arrest Specific 8 (Gas8) and G protein-coupled recept... 		MARK AS OVER ANNOTATED
Summary: The protein binding phenotype can occur downstream of altered SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear to be a direct activity of SMO.
Reason: Marked as over-annotated. The source (PMID:21659505; IPI experimental evidence) supports pathway perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling, and PKA-inhibitory functions.
Supporting Evidence:
PMID:21659505
Here we demonstrate that Growth Arrest Specific 8 (Gas8), a microtubule associated subunit of the Dynein Regulatory Complex (DRC), interacts with Smo to modulate this process.
GO:0005929 cilium
ISS
GO_REF:0000024 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
Cell projection, cilium membrane
GO:0005901 caveola
IDA
PMID:11278759
The sonic hedgehog receptor patched associates with caveolin... 		KEEP AS NON CORE
Summary: The caveola annotation is compatible with a context-specific localization, trafficking state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
Reason: Retained as non-core on the basis of IDA experimental evidence (PMID:11278759); it is secondary to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
Supporting Evidence:
PMID:11278759
both Smoothened and Patched are in caveolin-1-enriched/raft microdomains.
GO:0060170 ciliary membrane
TAS
Reactome:R-HSA-5633040 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The ciliary membrane annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
GO:0060170 ciliary membrane
TAS
Reactome:R-HSA-5632668 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The ciliary membrane annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
GO:0097542 ciliary tip
TAS
Reactome:R-HSA-5610763 		KEEP AS NON CORE
Summary: The ciliary tip annotation is compatible with a context-specific localization, trafficking state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
Reason: Retained as non-core on the basis of traceable-author-statement curation (Reactome:R-HSA-5610763); it is secondary to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
GO:0030666 endocytic vesicle membrane
TAS
Reactome:R-HSA-5610763 		KEEP AS NON CORE
Summary: The endocytic vesicle membrane annotation is compatible with a context-specific localization, trafficking state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
Reason: Retained as non-core on the basis of traceable-author-statement curation (Reactome:R-HSA-5610763); it is secondary to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
GO:0030666 endocytic vesicle membrane
TAS
Reactome:R-HSA-5632668 		KEEP AS NON CORE
Summary: The endocytic vesicle membrane annotation is compatible with a context-specific localization, trafficking state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
Reason: Retained as non-core on the basis of traceable-author-statement curation (Reactome:R-HSA-5632668); it is secondary to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
GO:0070062 extracellular exosome
HDA
PMID:23533145
In-depth proteomic analyses of exosomes isolated from expres... 		KEEP AS NON CORE
Summary: The extracellular exosome annotation is compatible with a context-specific localization, trafficking state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
Reason: Retained as non-core on the basis of high-throughput direct assay (PMID:23533145); it is secondary to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
GO:0070062 extracellular exosome
HDA
PMID:19056867
Large-scale proteomics and phosphoproteomics of urinary exos... 		KEEP AS NON CORE
Summary: The extracellular exosome annotation is compatible with a context-specific localization, trafficking state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
Reason: Retained as non-core on the basis of high-throughput direct assay (PMID:19056867); it is secondary to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
GO:0005794 Golgi apparatus
IDA
PMID:11278759
The sonic hedgehog receptor patched associates with caveolin... 		KEEP AS NON CORE
Summary: The Golgi apparatus annotation is compatible with a context-specific localization, trafficking state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
Reason: Retained as non-core on the basis of IDA experimental evidence (PMID:11278759); it is secondary to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
Supporting Evidence:
PMID:11278759
both Smoothened and Patched are in caveolin-1-enriched/raft microdomains.
GO:0071397 cellular response to cholesterol
ISS
GO_REF:0000024 		ACCEPT
Summary: SMO is the membrane transducer of the cellular response to cholesterol; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This curator-reviewed orthology transfer is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
file:human/SMO/SMO-uniprot.txt
G protein-coupled receptor, which transduces the smoothened signaling pathway
GO:0005929 cilium
TAS
PMID:21931618
The hedgehog receptor patched is involved in cholesterol tra... 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
GO:0005113 patched binding
IPI
PMID:9811851
Characterization of two patched receptors for the vertebrate... 		KEEP AS NON CORE
Summary: Patched proteins negatively regulate SMO and older biochemical experiments reported PTCH-SMO complexes. Current mechanistic work emphasizes control of SMO sterol access rather than a required stable receptor complex.
Reason: Retained as non-core because the physical association is reported by PMID:9811851 and supported phylogenetically, but patched binding is not the principal molecular activity of SMO.
Supporting Evidence:
PMID:9811851
they can form a complex with SMO.
GO:0007371 ventral midline determination
ISS
GO_REF:0000024 		KEEP AS NON CORE
Summary: The ventral midline determination annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:2000826 regulation of heart morphogenesis
ISS
GO_REF:0000024 		KEEP AS NON CORE
Summary: The regulation of heart morphogenesis annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0005886 plasma membrane
IDA
PMID:19304771
Evidence for allosteric interactions of antagonist binding t... 		ACCEPT
Summary: SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent accumulation in the membrane of the non-motile primary cilium. The plasma membrane annotation is consistent with this established trafficking and signaling cycle.
Reason: Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation occur.
Supporting Evidence:
PMID:19304771
Binding of two radioligands
GO:0007224 smoothened signaling pathway
IMP
PMID:19304771
Evidence for allosteric interactions of antagonist binding t... 		ACCEPT
Summary: SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IMP experimental evidence is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
PMID:19304771
Binding of two radioligands
GO:0007224 smoothened signaling pathway
IMP
PMID:21177415
Identification and mechanism of action of the acylguanidine ... 		ACCEPT
Summary: SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IMP experimental evidence is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
GO:0072285 mesenchymal to epithelial transition involved in metanephric renal vesicle formation
ISS
GO_REF:0000024 		KEEP AS NON CORE
Summary: The mesenchymal to epithelial transition involved in metanephric renal vesicle formation annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0090190 positive regulation of branching involved in ureteric bud morphogenesis
ISS
GO_REF:0000024 		KEEP AS NON CORE
Summary: The positive regulation of branching involved in ureteric bud morphogenesis annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0001947 heart looping
ISS
GO_REF:0000024 		KEEP AS NON CORE
Summary: The heart looping annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0003140 determination of left/right asymmetry in lateral mesoderm
ISS
GO_REF:0000024 		KEEP AS NON CORE
Summary: The determination of left/right asymmetry in lateral mesoderm annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0007224 smoothened signaling pathway
IEP
PMID:17850284
Immunohistochemical analysis of Sonic hedgehog signalling in... 		ACCEPT
Summary: Expression of SMO in the developing human urogenital sinus is consistent with operation of the smoothened signaling pathway during detrusor differentiation. Although IEP is weaker than a functional perturbation, the annotated pathway is the core signaling cascade directly transduced by SMO.
Reason: Accepted for consistency with the extensive direct biochemical and genetic evidence that SMO transduces this pathway. PMID:17850284 provides human developmental expression context rather than the sole basis for the mechanistic assignment.
Supporting Evidence:
PMID:17850284
The expression patterns of the SHH-transducing proteins Patched (PTCH) and Smoothened (SMO) were consistent with long-range paracrine signalling associated with detrusor smooth muscle differentiation in the urogenital sinus.
GO:0007494 midgut development
ISS
GO_REF:0000024 		KEEP AS NON CORE
Summary: The midgut development annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0048853 forebrain morphogenesis
ISS
GO_REF:0000024 		KEEP AS NON CORE
Summary: The forebrain morphogenesis annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0061053 somite development
ISS
GO_REF:0000024 		KEEP AS NON CORE
Summary: The somite development annotation records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is not the molecular activity that defines the protein.
Reason: Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary signal transduction.
GO:0007224 smoothened signaling pathway
IMP
PMID:9422511
Activating Smoothened mutations in sporadic basal-cell carci... 		ACCEPT
Summary: SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IMP experimental evidence is mechanistically concordant with direct human SMO studies.
Reason: Accepted as a core process annotation. The annotation names the signaling cascade or an immediate biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
Supporting Evidence:
PMID:9422511
These findings support the role of SMO as a signalling component of the SHH-receptor complex
GO:0060242 contact inhibition
IMP
PMID:9422511
Activating Smoothened mutations in sporadic basal-cell carci... 		UNDECIDED
Summary: The cited experimental annotation may be valid, but the cached publication record does not expose enough assay detail to verify the exact contact inhibition claim for human SMO.
Reason: Undecided because the relevant full text is unavailable locally. In accordance with the project policy, the experimental curator is not overruled from title/abstract-level evidence alone.
GO:0005515 protein binding
IPI
PMID:19592253
The mammalian Cos2 homolog Kif7 plays an essential role in m... 		UNDECIDED
Summary: The cited experimental annotation may be valid, but the cached publication record does not expose enough assay detail to verify the exact protein binding claim for human SMO.
Reason: Undecided because the relevant full text is unavailable locally. In accordance with the project policy, the experimental curator is not overruled from title/abstract-level evidence alone.
GO:0004862 cAMP-dependent protein kinase inhibitor activity
IDA
PMID:36202993
A PKA inhibitor motif within SMOOTHENED controls Hedgehog si... 		NEW
Summary: SMO contains a C-terminal PKI pseudosubstrate motif that directly occupies the PKA catalytic-subunit active site and inhibits its kinase activity, preventing inhibitory GLI phosphorylation.
Reason: Proposed because this specific molecular function is directly demonstrated in biochemical, cellular, and organismal assays in PMID:36202993 and is more informative than generic protein sequestering activity or PKA catalytic-subunit binding.
Supporting Evidence:
PMID:36202993
SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity.
PMID:39138140
GRK2 phosphorylation enables active SMO to bind PKA-C directly.

Core Functions

Sterol-regulated class-F G protein-coupled receptor activity that transduces Hedgehog input across the plasma and primary-cilium membranes. Active SMO couples to heterotrimeric Gi, lowering cellular cAMP, and promotes GLI activation.

Molecular Function:
G protein-coupled receptor activity
Directly Involved In:
smoothened signaling pathway adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
Cellular Locations:
plasma membrane non-motile cilium membrane
Supporting Evidence:
  • PMID:31168089
    We present a cryo-electron microscopy structure of human SMO bound to 24(S),25-epoxycholesterol and coupled to a heterotrimeric Gi protein.
  • PMID:32929279
    Smoothened (SMO), a class Frizzled G protein-coupled receptor (class F GPCR), transduces the Hedgehog signal across the cell membrane.

Cholesterol/sterol binding through the extracellular cysteine-rich domain and connected transmembrane sites; ligand occupancy and sterol movement stabilize signaling-competent SMO conformations required for native Hedgehog responses.

Molecular Function:
cholesterol binding
Directly Involved In:
smoothened signaling pathway
Cellular Locations:
plasma membrane non-motile cilium membrane
Supporting Evidence:
  • PMID:27437577
    Unexpectedly, we find a cholesterol molecule bound to Smoothened in the CRD binding site.
  • PMID:32929279
    These data indicate that sterol transport through the core of SMO is a major regulator of SMO-mediated signaling.

Direct cAMP-dependent protein kinase inhibitor activity: the phosphorylated C-terminal SMO PKI motif acts as a pseudosubstrate that binds the PKA catalytic-subunit active site, sequesters and inhibits PKA-C, and thereby prevents inhibitory GLI phosphorylation during Hedgehog signaling.

Molecular Function:
cAMP-dependent protein kinase inhibitor activity
Directly Involved In:
smoothened signaling pathway
Cellular Locations:
non-motile cilium membrane
Supporting Evidence:
  • PMID:36202993
    SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity.
  • PMID:39138140
    GRK2 phosphorylation enables active SMO to bind PKA-C directly.

References

GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms
GO_REF:0000024
Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity
GO_REF:0000033
Annotation inferences using phylogenetic trees
GO_REF:0000044
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
GO_REF:0000052
Gene Ontology annotation based on curation of immunofluorescence data
GO_REF:0000107
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
GO_REF:0000117
Electronic Gene Ontology annotations created by ARBA machine learning models
GO_REF:0000120
Combined Automated Annotation using Multiple IEA Methods
PMID:11278759
The sonic hedgehog receptor patched associates with caveolin-1 in cholesterol-rich microdomains of the plasma membrane.
PMID:17850284
Immunohistochemical analysis of Sonic hedgehog signalling in normal human urinary tract development.
PMID:19056867
Large-scale proteomics and phosphoproteomics of urinary exosomes.
PMID:19304771
Evidence for allosteric interactions of antagonist binding to the smoothened receptor.
PMID:19592253
The mammalian Cos2 homolog Kif7 plays an essential role in modulating Hh signal transduction during development.
PMID:21177415
Identification and mechanism of action of the acylguanidine MRT-83, a novel potent Smoothened antagonist.
PMID:21659505
Growth Arrest Specific 8 (Gas8) and G protein-coupled receptor kinase 2 (GRK2) cooperate in the control of Smoothened signaling.
PMID:21671467
miR-338-3p suppresses invasion of liver cancer cell by targeting smoothened.
PMID:21931618
The hedgehog receptor patched is involved in cholesterol transport.
PMID:22072986
A novel protein LZTFL1 regulates ciliary trafficking of the BBSome and Smoothened.
  • Endogenous SMO accumulates in primary cilia in response to agonist, with BBSome/LZTFL1 controlling its ciliary trafficking.
    "In control siRNA transfected cells, SMO localizes to the cilia in response to SMO agonist (SAG) but not in SAG-untreated cells"
PMID:23533145
In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine.
PMID:27437577
Structural basis of Smoothened regulation by its extracellular domains.
  • Human SMO contains a cholesterol-binding site in its extracellular cysteine-rich domain, and mutations that disrupt cholesterol binding impair native Hedgehog signal transmission.
    "Unexpectedly, we find a cholesterol molecule bound to Smoothened in the CRD binding site."
PMID:27727273
Zfp423 Regulates Sonic Hedgehog Signaling via Primary Cilium Function.
PMID:31168089
Cryo-EM structure of oxysterol-bound human Smoothened coupled to a heterotrimeric G(i).
  • Oxysterol-bound human SMO directly couples to heterotrimeric Gi and activates Gi-dependent Hedgehog signaling.
    "We present a cryo-electron microscopy structure of human SMO bound to 24(S),25-epoxycholesterol and coupled to a heterotrimeric Gi protein."
PMID:32413283
Bi-allelic Variations of SMO in Humans Cause a Broad Spectrum of Developmental Anomalies Due to Abnormal Hedgehog Signaling.
  • Biallelic human SMO loss-of-function variants disrupt primary-cilium pathway dynamics and cause multisystem developmental anomalies.
    "Cells derived from affected individuals showed normal ciliogenesis but severely altered Hh-signal transduction as a result of either altered PC trafficking or abnormal activation of the pathway downstream of SMO."
PMID:32929279
Sterols in an intramolecular channel of Smoothened mediate Hedgehog signaling.
  • Sterols occupy connected binding sites within SMO and regulate its active signaling conformation.
    "These data indicate that sterol transport through the core of SMO is a major regulator of SMO-mediated signaling."
PMID:36202993
A PKA inhibitor motif within SMOOTHENED controls Hedgehog signal transduction.
  • The SMO PKI pseudosubstrate motif directly inhibits PKA catalytic activity and is required for Hedgehog signal transduction.
    "SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity."
PMID:39138140
GRK2 kinases in the primary cilium initiate SMOOTHENED-PKA signaling in the Hedgehog cascade.
  • GRK2 phosphorylation of active ciliary SMO triggers direct PKA-C binding and inactivation during endogenous Hedgehog signaling.
    "GRK2 phosphorylation enables active SMO to bind PKA-C directly."
PMID:9422511
Activating Smoothened mutations in sporadic basal-cell carcinoma.
  • Activating human SMO mutations drive Hedgehog-pathway signaling and oncogenic transformation.
    "These findings support the role of SMO as a signalling component of the SHH-receptor complex"
PMID:9811851
Characterization of two patched receptors for the vertebrate hedgehog protein family.
  • Biochemical analysis reported that PTCH1 and PTCH2 can form complexes with SMO.
    "they can form a complex with SMO."
Reactome:R-HSA-5610763
PTCH1 inhibits accumulation of SMO in the primary cilium in the absence of Hh signal
Reactome:R-HSA-5632668
SMO translocates to the cilium
Reactome:R-HSA-5633040
CSNK1A1 and ADRBK1 dissociate from p-SMO dimer
file:human/SMO/SMO-uniprot.txt
UniProtKB reviewed record for human SMO (Q99835)
  • SMO is a sterol-activated GPCR that signals through Gi and direct PKA-C sequestration at plasma and ciliary membranes.
    "G protein-coupled receptor, which transduces the smoothened signaling pathway"

Suggested Questions for Experts

Q: In which human cell types does SMO signal predominantly through heterotrimeric Gi versus direct PKA-C inhibition, and how are these two immediate effector routes integrated?

Q: Which endogenous cholesterol or oxysterol species occupies each SMO sterol-binding site in specific physiological tissues?

Suggested Experiments

Experiment: Introduce endogenous separation-of-function SMO alleles that selectively disrupt Gi coupling or the PKI pseudosubstrate motif in human ciliated neural and mesenchymal organoids. Measure ciliary SMO trafficking, local and whole-cell cAMP, PKA substrate phosphorylation, GLI processing, and GLI target transcription after defined SHH and sterol stimulation, with wild-type rescue controls.

Hypothesis: Gi coupling and PKI-motif-dependent PKA inhibition make separable, cell-context-dependent contributions to human SMO-to-GLI signaling.

Type: CRISPR knock-in with live-cell signaling and organoid phenotyping

📚 Additional Documentation

Notes

(SMO-notes.md)

SMO review notes

Scope and sources

This journal records the manual review of the 98 seeded human SMO GO annotations plus one proposed new molecular-function annotation. I inspected the reviewed UniProtKB record Q99835, the complete GOA seed, every locally cached publication cited by GOA, and the current official GO records used in core_functions. No deep-research provider output was available: the previously attempted Falcon and Perplexity-lite calls failed, so they were not retried and no provider-named report was created.

The official QuickGO service was checked on 2026-07-14 for the author-supplied core-function terms. It returned current, non-obsolete records for GO:0004930 “G protein-coupled receptor activity,” GO:0015485 “cholesterol binding,” GO:0004862 “cAMP-dependent protein kinase inhibitor activity,” GO:0007224 “smoothened signaling pathway,” and GO:0098804 “non-motile cilium membrane.”

Project-independent molecular model

SMO is a class-F seven-pass GPCR and the membrane transducer between Patched/sterol control and GLI activation. Direct structural work describes it as a Frizzled-class GPCR and shows oxysterol-bound human SMO coupled to heterotrimeric Gi [PMID:31168089 “We present a cryo-electron microscopy structure of human SMO bound to 24(S),25-epoxycholesterol and coupled to a heterotrimeric Gi protein.”]. In the same study, 24(S),25-epoxycholesterol stimulated Gi activation through SMO, supporting the GPCR activity and adenylate-cyclase-inhibiting pathway annotations rather than relying only on family classification.

Sterol binding is mechanistically integral, not an incidental ligand interaction. Human SMO structures identified cholesterol in the extracellular cysteine-rich-domain pocket [PMID:27437577 “Unexpectedly, we find a cholesterol molecule bound to Smoothened in the CRD binding site.”], and mutations predicted to disrupt this binding impaired native Hh signal transmission. Later structural work mapped connected sterol sites through the receptor and concluded that sterol movement regulates signaling [PMID:32929279 “These data indicate that sterol transport through the core of SMO is a major regulator of SMO-mediated signaling.”]. I therefore retained cholesterol and oxysterol binding and represented cholesterol binding as a distinct core molecular function.

The current evidence also establishes a second immediate effector mechanism beyond Gi. SMO's C-terminal PKI motif acts as a pseudosubstrate that occupies the PKA catalytic active site [PMID:36202993 “SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity.”]. Follow-up work showed that GRK2 phosphorylation enables direct active-SMO/PKA-C binding in cilia [PMID:39138140 “GRK2 phosphorylation enables active SMO to bind PKA-C directly.”]. This evidence supports PKA catalytic-subunit binding and protein sequestering activity, but the more informative molecular function is GO:0004862, “cAMP-dependent protein kinase inhibitor activity.” I added it as a proposed NEW annotation and made it a core function.

Functional location and trafficking

The signaling-competent locations are the plasma membrane and non-motile primary-cilium membrane. Human RPE1-cell experiments show agonist-dependent endogenous SMO entry into cilia [PMID:22072986 “In control siRNA transfected cells, SMO localizes to the cilia in response to SMO agonist (SAG) but not in SAG-untreated cells”]. BBSome/LZTFL1 perturbations alter that trafficking, while the 2024 GRK2 study places SMO phosphorylation and PKA-C engagement in the cilium. These observations justify accepting plasma-membrane, cilium, ciliary-membrane, and non-motile-cilium-membrane annotations.

Endocytic-vesicle membrane, Golgi, ciliary tip, caveolar/raft microdomains, dendrite, and extracellular-exosome detections were retained as non-core locations. The caveolar/raft paper directly reports that both proteins occur in caveolin-enriched microdomains [PMID:11278759 “both Smoothened and Patched are in caveolin-1-enriched/raft microdomains.”], but this is a trafficking/localization context, not a defining SMO activity. The urinary and prostatic exosome terms come from high-throughput proteomics and likewise do not identify a signaling site.

Patched relationship

Older biochemical work reported PTCH1 and PTCH2 complexes with SMO [PMID:9811851 “they can form a complex with SMO.”], so the patched-binding annotations were retained rather than rejected. They are non-core because the modern mechanism is primarily indirect: Patched regulates availability/access of activating sterols, and stable PTCH-SMO binding is not required to explain pathway control. This distinction avoids treating a historical co-complex observation as the central molecular function.

Development and disease evidence

SMO's core biochemistry is deployed broadly in morphogen interpretation. The IBA/ISS/IEA annotations for CNS development, pattern specification, commissural axon guidance, neural-tube patterning, left-right asymmetry, heart, somite, gut, forebrain, and urinary-system morphogenesis are biologically coherent context-specific outputs and were retained as non-core rather than promoted to defining functions.

Human genetic evidence strongly supports pleiotropic developmental importance. Individuals with biallelic loss-of-function variants had brain, heart, skeletal, and enteric nervous-system anomalies, and patient-derived cells showed altered Hh signal transduction/primary-cilium pathway dynamics [PMID:32413283 “Cells derived from affected individuals showed normal ciliogenesis but severely altered Hh-signal transduction as a result of either altered PC trafficking or abnormal activation of the pathway downstream of SMO.”]. Activating SMO variants provide reciprocal evidence for pathway activation and oncogenesis [PMID:9422511 “These findings support the role of SMO as a signalling component of the SHH-receptor complex”].

The developing urinary-tract paper is expression-based rather than a perturbation study. It found SMO/PTCH patterns consistent with paracrine signaling during detrusor smooth-muscle differentiation [PMID:17850284 “The expression patterns of the SHH-transducing proteins Patched (PTCH) and Smoothened (SMO) were consistent with long-range paracrine signalling associated with detrusor smooth muscle differentiation in the urogenital sinus.”]. I retained smooth-muscle development as non-core and accepted the smoothened-pathway term because that pathway assignment is independently established by extensive direct evidence.

Annotation triage decisions

  • Broad transmembrane signaling receptor activity, cell surface receptor signaling pathway, membrane, and plasma membrane bounded cell projection annotations were modified to the experimentally established GPCR/pathway/plasma-or-ciliary terms.
  • Broad tissue development, whole-organism growth, organ growth, and generic positive/negative transcription annotations were marked over-annotated because they conflate downstream GLI-dependent outcomes with SMO's direct activity.
  • The liver-cancer migration and gene-expression IMP annotations were marked over-annotated. The study shows that miR-338-3p targets SMO and that SMO knockdown reverses invasion-related readouts [PMID:21671467 “small interfering RNA targeted SMO reversed the effects induced by blockade of miR-338-3p.”], but migration and generic gene-expression regulation are indirect pathway outputs.
  • The generic protein binding annotation supported by Gas8 interaction was marked over-annotated because the physical interaction is real [PMID:21659505 “Here we demonstrate that Growth Arrest Specific 8 (Gas8), a microtubule associated subunit of the Dynein Regulatory Complex (DRC), interacts with Smo to modulate this process.”] but protein binding is not informative about SMO function.
  • The KIF7 protein binding IPI and the contact inhibition IMP were left UNDECIDED. Their cached papers are abstract-only and do not expose enough assay detail to verify those exact claims. The experimental curators were not overruled.

Remaining mechanistic questions

The major unresolved issue is how much heterotrimeric-Gi coupling versus direct PKI-motif-mediated PKA inhibition contributes to SMO-to-GLI signaling in different human tissues. A second question is which endogenous sterol occupies each SMO site in each physiological context. Separation-of-function endogenous alleles, assayed in multiple human ciliated organoid lineages with local cAMP, PKA, GLI-processing, and transcriptional readouts, would distinguish these branches without conflating them with downstream developmental phenotypes.

📄 View Raw YAML

 
---
id: Q99835
gene_symbol: SMO
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  SMO (Smoothened) is a 787-amino-acid, seven-pass class-F G protein-coupled receptor and the obligate
  signal-transducing membrane component of vertebrate Hedgehog signaling. In the pathway-off state, PTCH1
  or PTCH2 restricts SMO access to activating sterols. Hedgehog binding to Patched relieves this inhibition,
  allowing cholesterol and oxysterols to bind SMO's extracellular cysteine-rich domain and transmembrane
  sterol-binding sites, stabilize an active conformation, and promote accumulation of SMO in the primary-cilium
  membrane. Active SMO can couple to heterotrimeric Gi, lowering cAMP, and also directly binds and inhibits
  the catalytic subunit of protein kinase A through a C-terminal pseudosubstrate/PKI motif. These mechanisms
  prevent inhibitory phosphorylation and processing of GLI transcription factors and permit GLI-dependent
  transcription. SMO therefore functions principally at the plasma membrane and the membrane of non-motile
  primary cilia, with context-dependent roles in embryonic patterning, organogenesis, tissue homeostasis,
  and cell proliferation. Germline biallelic loss-of-function variants cause pleiotropic developmental
  anomalies through impaired Hedgehog signaling, whereas activating somatic or mosaic variants drive tumors
  and Curry-Jones syndrome.
existing_annotations:
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The plasma membrane annotation is
      consistent with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: Cell membrane
- term:
    id: GO:0005929
    label: cilium
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent
      with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: Cell projection, cilium membrane
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This phylogenetic inference
      is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: G protein-coupled receptor, which transduces the smoothened signaling pathway
- term:
    id: GO:0007417
    label: central nervous system development
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      The central nervous system development annotation records a conserved, context-specific developmental
      output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this
      tissue-level process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The phylogenetic inference (GO_REF:0000033) is biologically plausible and
      consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0007389
    label: pattern specification process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      The pattern specification process annotation records a conserved, context-specific developmental
      output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this
      tissue-level process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The phylogenetic inference (GO_REF:0000033) is biologically plausible and
      consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0030425
    label: dendrite
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: >-
      The dendrite annotation is compatible with a context-specific localization, trafficking state, or
      downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
    reason: >-
      Retained as non-core on the basis of phylogenetic inference (GO_REF:0000033); it is secondary to
      SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0071679
    label: commissural neuron axon guidance
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: >-
      The commissural neuron axon guidance annotation records a conserved, context-specific developmental
      output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this
      tissue-level process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The phylogenetic inference (GO_REF:0000033) is biologically plausible and
      consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005113
    label: patched binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: >-
      Patched proteins negatively regulate SMO and older biochemical experiments reported PTCH-SMO complexes.
      Current mechanistic work emphasizes control of SMO sterol access rather than a required stable receptor
      complex.
    reason: >-
      Retained as non-core because the physical association is reported by PMID:9811851 and supported
      phylogenetically, but patched binding is not the principal molecular activity of SMO.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0004888
    label: transmembrane signaling receptor activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: >-
      The transmembrane signaling receptor activity annotation is directionally correct but too broad
      to represent SMO's established function. SMO is a sterol-regulated class-F GPCR that transduces
      the smoothened pathway at plasma and ciliary membranes.
    reason: >-
      Modify to the more informative G protein-coupled receptor activity (GO:0004930). The replacement
      preserves the source inference (GO_REF:0000002) while matching the experimentally established specificity
      of SMO.
    proposed_replacement_terms:
    - id: GO:0004930
      label: G protein-coupled receptor activity
    action: MODIFY
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The plasma membrane annotation is
      consistent with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
- term:
    id: GO:0007166
    label: cell surface receptor signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      The cell surface receptor signaling pathway annotation is directionally correct but too broad to
      represent SMO's established function. SMO is a sterol-regulated class-F GPCR that transduces the
      smoothened pathway at plasma and ciliary membranes.
    reason: >-
      Modify to the more informative smoothened signaling pathway (GO:0007224). The replacement preserves
      the source inference (GO_REF:0000002) while matching the experimentally established specificity
      of SMO.
    proposed_replacement_terms:
    - id: GO:0007224
      label: smoothened signaling pathway
    action: MODIFY
- term:
    id: GO:0009888
    label: tissue development
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >-
      The tissue development phenotype can occur downstream of altered SMO/Hedgehog signaling, but the
      annotation makes an indirect cellular or organismal output appear to be a direct activity of SMO.
    reason: >-
      Marked as over-annotated. The source (GO_REF:0000117; electronic inference) supports pathway perturbation
      or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling,
      and PKA-inhibitory functions.
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: located_in
  review:
    summary: >-
      The membrane annotation is directionally correct but too broad to represent SMO's established function.
      SMO is a sterol-regulated class-F GPCR that transduces the smoothened pathway at plasma and ciliary
      membranes.
    reason: >-
      Modify to the more informative plasma membrane (GO:0005886) and ciliary membrane (GO:0060170). The
      replacement preserves the source inference (GO_REF:0000002) while matching the experimentally established
      specificity of SMO.
    proposed_replacement_terms:
    - id: GO:0005886
      label: plasma membrane
    - id: GO:0060170
      label: ciliary membrane
    action: MODIFY
- term:
    id: GO:0060170
    label: ciliary membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The ciliary membrane annotation is
      consistent with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
- term:
    id: GO:0120025
    label: plasma membrane bounded cell projection
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: located_in
  review:
    summary: >-
      The plasma membrane bounded cell projection annotation is directionally correct but too broad to
      represent SMO's established function. SMO is a sterol-regulated class-F GPCR that transduces the
      smoothened pathway at plasma and ciliary membranes.
    reason: >-
      Modify to the more informative cilium (GO:0005929). The replacement preserves the source inference
      (GO_REF:0000117) while matching the experimentally established specificity of SMO.
    proposed_replacement_terms:
    - id: GO:0005929
      label: cilium
    action: MODIFY
- term:
    id: GO:0001947
    label: heart looping
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The heart looping annotation records a conserved, context-specific developmental output of Hedgehog/SMO
      signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is
      not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent
      with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary
      signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0003140
    label: determination of left/right asymmetry in lateral mesoderm
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The determination of left/right asymmetry in lateral mesoderm annotation records a conserved, context-specific
      developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation,
      but this tissue-level process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent
      with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary
      signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0004930
    label: G protein-coupled receptor activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      The G protein-coupled receptor activity annotation captures a directly established molecular activity
      of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural,
      biochemical, and cellular studies; this electronic inference is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000107) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: G protein-coupled receptor, which transduces the smoothened signaling pathway
- term:
    id: GO:0005929
    label: cilium
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: part_of
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent
      with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: Cell projection, cilium membrane
- term:
    id: GO:0007193
    label: adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the adenylate cyclase-inhibiting G protein-coupled receptor signaling
      pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits
      GLI activation. This electronic inference is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: G protein-coupled receptor, which transduces the smoothened signaling pathway
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This electronic inference
      is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: G protein-coupled receptor, which transduces the smoothened signaling pathway
- term:
    id: GO:0007371
    label: ventral midline determination
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The ventral midline determination annotation records a conserved, context-specific developmental
      output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this
      tissue-level process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent
      with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary
      signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0007494
    label: midgut development
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The midgut development annotation records a conserved, context-specific developmental output of
      Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level
      process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent
      with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary
      signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0008142
    label: oxysterol binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      The oxysterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated
      class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and
      cellular studies; this electronic inference is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000107) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: In addition to cholesterol, SMO is also activated by various oxysterols
- term:
    id: GO:0015485
    label: cholesterol binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      The cholesterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated
      class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and
      cellular studies; this electronic inference is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000107) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: G protein-coupled receptor, which transduces the smoothened signaling pathway
- term:
    id: GO:0021513
    label: spinal cord dorsal/ventral patterning
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The spinal cord dorsal/ventral patterning annotation records a conserved, context-specific developmental
      output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this
      tissue-level process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent
      with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary
      signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0034236
    label: protein kinase A catalytic subunit binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      The protein kinase A catalytic subunit binding annotation captures a directly established molecular
      activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported
      by structural, biochemical, and cellular studies; this electronic inference is concordant with that
      mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000107) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: Interacts (via PKI motif) with protein kinase A catalytic subunit PRKACA
- term:
    id: GO:0040018
    label: positive regulation of multicellular organism growth
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The positive regulation of multicellular organism growth phenotype can occur downstream of altered
      SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear
      to be a direct activity of SMO.
    reason: >-
      Marked as over-annotated. The source (GO_REF:0000107; electronic inference) supports pathway perturbation
      or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling,
      and PKA-inhibitory functions.
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0045880
    label: positive regulation of smoothened signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the positive regulation of smoothened signaling pathway; activation
      by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation.
      This electronic inference is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: G protein-coupled receptor, which transduces the smoothened signaling pathway
- term:
    id: GO:0045892
    label: negative regulation of DNA-templated transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The negative regulation of DNA-templated transcription phenotype can occur downstream of altered
      SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear
      to be a direct activity of SMO.
    reason: >-
      Marked as over-annotated. The source (GO_REF:0000107; electronic inference) supports pathway perturbation
      or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling,
      and PKA-inhibitory functions.
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0045893
    label: positive regulation of DNA-templated transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The positive regulation of DNA-templated transcription phenotype can occur downstream of altered
      SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output appear
      to be a direct activity of SMO.
    reason: >-
      Marked as over-annotated. The source (GO_REF:0000107; electronic inference) supports pathway perturbation
      or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling,
      and PKA-inhibitory functions.
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0046622
    label: positive regulation of organ growth
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The positive regulation of organ growth phenotype can occur downstream of altered SMO/Hedgehog signaling,
      but the annotation makes an indirect cellular or organismal output appear to be a direct activity
      of SMO.
    reason: >-
      Marked as over-annotated. The source (GO_REF:0000107; electronic inference) supports pathway perturbation
      or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding, Gi-coupling,
      and PKA-inhibitory functions.
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0048853
    label: forebrain morphogenesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The forebrain morphogenesis annotation records a conserved, context-specific developmental output
      of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level
      process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent
      with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary
      signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0061053
    label: somite development
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The somite development annotation records a conserved, context-specific developmental output of
      Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level
      process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent
      with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary
      signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0071397
    label: cellular response to cholesterol
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the cellular response to cholesterol; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This electronic inference
      is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: G protein-coupled receptor, which transduces the smoothened signaling pathway
- term:
    id: GO:0072285
    label: mesenchymal to epithelial transition involved in metanephric renal vesicle formation
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The mesenchymal to epithelial transition involved in metanephric renal vesicle formation annotation
      records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required
      broadly for morphogen interpretation, but this tissue-level process is not the molecular activity
      that defines the protein.
    reason: >-
      Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent
      with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary
      signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0090190
    label: positive regulation of branching involved in ureteric bud morphogenesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The positive regulation of branching involved in ureteric bud morphogenesis annotation records a
      conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly
      for morphogen interpretation, but this tissue-level process is not the molecular activity that defines
      the protein.
    reason: >-
      Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent
      with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary
      signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0098804
    label: non-motile cilium membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The non-motile cilium membrane annotation
      is consistent with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: Cell projection, cilium membrane
- term:
    id: GO:0140311
    label: protein sequestering activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: enables
  review:
    summary: >-
      The protein sequestering activity annotation captures a directly established molecular activity
      of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural,
      biochemical, and cellular studies; this electronic inference is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000107) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: Interacts (via PKI motif) with protein kinase A catalytic subunit PRKACA
- term:
    id: GO:2000826
    label: regulation of heart morphogenesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: involved_in
  review:
    summary: >-
      The regulation of heart morphogenesis annotation records a conserved, context-specific developmental
      output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this
      tissue-level process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The electronic inference (GO_REF:0000107) is biologically plausible and consistent
      with SMO's pleiotropic developmental role, while the core function remains sterol-regulated ciliary
      signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0004930
    label: G protein-coupled receptor activity
  evidence_type: IDA
  original_reference_id: PMID:27437577
  qualifier: enables
  review:
    summary: >-
      The G protein-coupled receptor activity annotation captures a directly established molecular activity
      of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural,
      biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (PMID:27437577) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:27437577
      supporting_text: Unexpectedly, we find a cholesterol molecule bound to Smoothened in the CRD binding
        site.
- term:
    id: GO:0004930
    label: G protein-coupled receptor activity
  evidence_type: IDA
  original_reference_id: PMID:31168089
  qualifier: enables
  review:
    summary: >-
      The G protein-coupled receptor activity annotation captures a directly established molecular activity
      of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural,
      biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (PMID:31168089) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:31168089
      supporting_text: >-
        The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F),
        transduces the Hedgehog signal
- term:
    id: GO:0004930
    label: G protein-coupled receptor activity
  evidence_type: IDA
  original_reference_id: PMID:32929279
  qualifier: enables
  review:
    summary: >-
      The G protein-coupled receptor activity annotation captures a directly established molecular activity
      of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural,
      biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (PMID:32929279) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:32929279
      supporting_text: >-
        Smoothened (SMO), a class Frizzled G protein-coupled receptor (class F GPCR), transduces the Hedgehog
        signal across the cell membrane.
- term:
    id: GO:0007193
    label: adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:32929279
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the adenylate cyclase-inhibiting G protein-coupled receptor signaling
      pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits
      GLI activation. This IDA experimental evidence is mechanistically concordant with direct human SMO
      studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:32929279
      supporting_text: >-
        Smoothened (SMO), a class Frizzled G protein-coupled receptor (class F GPCR), transduces the Hedgehog
        signal across the cell membrane.
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:31168089
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IDA experimental
      evidence is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:31168089
      supporting_text: >-
        The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F),
        transduces the Hedgehog signal
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:32929279
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IDA experimental
      evidence is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:32929279
      supporting_text: >-
        Smoothened (SMO), a class Frizzled G protein-coupled receptor (class F GPCR), transduces the Hedgehog
        signal across the cell membrane.
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:39138140
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IDA experimental
      evidence is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:39138140
      supporting_text: GRK2 phosphorylation enables active SMO to bind PKA-C directly.
- term:
    id: GO:0015485
    label: cholesterol binding
  evidence_type: IDA
  original_reference_id: PMID:27437577
  qualifier: enables
  review:
    summary: >-
      The cholesterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated
      class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and
      cellular studies; this IDA experimental evidence is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (PMID:27437577) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:27437577
      supporting_text: Unexpectedly, we find a cholesterol molecule bound to Smoothened in the CRD binding
        site.
- term:
    id: GO:0015485
    label: cholesterol binding
  evidence_type: IDA
  original_reference_id: PMID:31168089
  qualifier: enables
  review:
    summary: >-
      The cholesterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated
      class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and
      cellular studies; this IDA experimental evidence is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (PMID:31168089) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:31168089
      supporting_text: >-
        The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F),
        transduces the Hedgehog signal
- term:
    id: GO:0015485
    label: cholesterol binding
  evidence_type: IDA
  original_reference_id: PMID:32929279
  qualifier: enables
  review:
    summary: >-
      The cholesterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated
      class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and
      cellular studies; this IDA experimental evidence is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (PMID:32929279) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:32929279
      supporting_text: >-
        Smoothened (SMO), a class Frizzled G protein-coupled receptor (class F GPCR), transduces the Hedgehog
        signal across the cell membrane.
- term:
    id: GO:0140311
    label: protein sequestering activity
  evidence_type: IDA
  original_reference_id: PMID:39138140
  qualifier: enables
  review:
    summary: >-
      The protein sequestering activity annotation captures a directly established molecular activity
      of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural,
      biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (PMID:39138140) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:39138140
      supporting_text: GRK2 phosphorylation enables active SMO to bind PKA-C directly.
- term:
    id: GO:0007193
    label: adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:31168089
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the adenylate cyclase-inhibiting G protein-coupled receptor signaling
      pathway; activation by sterols couples SMO to Gi and/or direct PKA-C inhibition and thereby permits
      GLI activation. This IDA experimental evidence is mechanistically concordant with direct human SMO
      studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:31168089
      supporting_text: >-
        The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F),
        transduces the Hedgehog signal
- term:
    id: GO:0098804
    label: non-motile cilium membrane
  evidence_type: IDA
  original_reference_id: PMID:31168089
  qualifier: is_active_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The non-motile cilium membrane annotation
      is consistent with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:31168089
      supporting_text: >-
        The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F),
        transduces the Hedgehog signal
- term:
    id: GO:0140311
    label: protein sequestering activity
  evidence_type: IDA
  original_reference_id: PMID:36202993
  qualifier: enables
  review:
    summary: >-
      The protein sequestering activity annotation captures a directly established molecular activity
      of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported by structural,
      biochemical, and cellular studies; this IDA experimental evidence is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (PMID:36202993) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:36202993
      supporting_text: >-
        SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent
        protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity.
- term:
    id: GO:0098804
    label: non-motile cilium membrane
  evidence_type: IDA
  original_reference_id: PMID:22072986
  qualifier: is_active_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The non-motile cilium membrane annotation
      is consistent with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:22072986
      supporting_text: >-
        In control siRNA transfected cells, SMO localizes to the cilia in response to SMO agonist (SAG)
        but not in SAG-untreated cells
- term:
    id: GO:0005929
    label: cilium
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent
      with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The plasma membrane annotation is
      consistent with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: Cell membrane
- term:
    id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: acts_upstream_of
  review:
    summary: >-
      The positive regulation of transcription by RNA polymerase II phenotype can occur downstream of
      altered SMO/Hedgehog signaling, but the annotation makes an indirect cellular or organismal output
      appear to be a direct activity of SMO.
    reason: >-
      Marked as over-annotated. The source (GO_REF:0000024; curator-reviewed orthology transfer) supports
      pathway perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer,
      sterol-binding, Gi-coupling, and PKA-inhibitory functions.
    action: MARK_AS_OVER_ANNOTATED
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:36202993
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IDA experimental
      evidence is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:36202993
      supporting_text: >-
        SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent
        protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity.
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This curator-reviewed
      orthology transfer is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: G protein-coupled receptor, which transduces the smoothened signaling pathway
- term:
    id: GO:0034236
    label: protein kinase A catalytic subunit binding
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      The protein kinase A catalytic subunit binding annotation captures a directly established molecular
      activity of SMO. Sterol-regulated class-F GPCR signaling and direct PKA-C engagement are supported
      by structural, biochemical, and cellular studies; this curator-reviewed orthology transfer is concordant
      with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000024) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: Interacts (via PKI motif) with protein kinase A catalytic subunit PRKACA
- term:
    id: GO:0008142
    label: oxysterol binding
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: >-
      The oxysterol binding annotation captures a directly established molecular activity of SMO. Sterol-regulated
      class-F GPCR signaling and direct PKA-C engagement are supported by structural, biochemical, and
      cellular studies; this curator-reviewed orthology transfer is concordant with that mechanism.
    reason: >-
      Accepted as part of SMO's core molecular mechanism. The source (GO_REF:0000024) is consistent with
      direct human SMO evidence summarized in PMID:27437577, PMID:31168089, PMID:32929279, PMID:36202993,
      and PMID:39138140, as applicable to this activity.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: In addition to cholesterol, SMO is also activated by various oxysterols
- term:
    id: GO:0005929
    label: cilium
  evidence_type: IDA
  original_reference_id: PMID:32413283
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent
      with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:32413283
      supporting_text: >-
        Cells derived from affected individuals showed normal ciliogenesis but severely altered Hh-signal
        transduction as a result of either altered PC trafficking or abnormal activation of the pathway
        downstream of SMO.
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:32413283
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IMP experimental
      evidence is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:32413283
      supporting_text: >-
        Cells derived from affected individuals showed normal ciliogenesis but severely altered Hh-signal
        transduction as a result of either altered PC trafficking or abnormal activation of the pathway
        downstream of SMO.
- term:
    id: GO:0005929
    label: cilium
  evidence_type: IDA
  original_reference_id: PMID:27727273
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent
      with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:27727273
      supporting_text: >-
        loss of Zfp423 in these precursors leads to cell-intrinsic reduction in proliferation, loss of
        response to Shh, and primary cilia abnormalities that include diminished frequency of both Smoothened
        and IFT88 localization.
- term:
    id: GO:0048745
    label: smooth muscle tissue development
  evidence_type: IEP
  original_reference_id: PMID:17850284
  qualifier: involved_in
  review:
    summary: >-
      The smooth muscle tissue development annotation records a conserved, context-specific developmental
      output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this
      tissue-level process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The expression-pattern evidence (PMID:17850284) is biologically plausible
      and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:17850284
      supporting_text: >-
        The expression patterns of the SHH-transducing proteins Patched (PTCH) and Smoothened (SMO) were
        consistent with long-range paracrine signalling associated with detrusor smooth muscle differentiation
        in the urogenital sinus.
- term:
    id: GO:0010628
    label: positive regulation of gene expression
  evidence_type: IMP
  original_reference_id: PMID:21671467
  qualifier: involved_in
  review:
    summary: >-
      The positive regulation of gene expression phenotype can occur downstream of altered SMO/Hedgehog
      signaling, but the annotation makes an indirect cellular or organismal output appear to be a direct
      activity of SMO.
    reason: >-
      Marked as over-annotated. The source (PMID:21671467; IMP experimental evidence) supports pathway
      perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding,
      Gi-coupling, and PKA-inhibitory functions.
    action: MARK_AS_OVER_ANNOTATED
    supported_by:
    - reference_id: PMID:21671467
      supporting_text: small interfering RNA targeted SMO reversed the effects induced by blockade of
        miR-338-3p.
- term:
    id: GO:0030335
    label: positive regulation of cell migration
  evidence_type: IMP
  original_reference_id: PMID:21671467
  qualifier: involved_in
  review:
    summary: >-
      The positive regulation of cell migration phenotype can occur downstream of altered SMO/Hedgehog
      signaling, but the annotation makes an indirect cellular or organismal output appear to be a direct
      activity of SMO.
    reason: >-
      Marked as over-annotated. The source (PMID:21671467; IMP experimental evidence) supports pathway
      perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding,
      Gi-coupling, and PKA-inhibitory functions.
    action: MARK_AS_OVER_ANNOTATED
    supported_by:
    - reference_id: PMID:21671467
      supporting_text: small interfering RNA targeted SMO reversed the effects induced by blockade of
        miR-338-3p.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21659505
  qualifier: enables
  review:
    summary: >-
      The protein binding phenotype can occur downstream of altered SMO/Hedgehog signaling, but the annotation
      makes an indirect cellular or organismal output appear to be a direct activity of SMO.
    reason: >-
      Marked as over-annotated. The source (PMID:21659505; IPI experimental evidence) supports pathway
      perturbation or a downstream phenotype, whereas SMO directly performs receptor/transducer, sterol-binding,
      Gi-coupling, and PKA-inhibitory functions.
    action: MARK_AS_OVER_ANNOTATED
    supported_by:
    - reference_id: PMID:21659505
      supporting_text: >-
        Here we demonstrate that Growth Arrest Specific 8 (Gas8), a microtubule associated subunit of
        the Dynein Regulatory Complex (DRC), interacts with Smo to modulate this process.
- term:
    id: GO:0005929
    label: cilium
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent
      with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: Cell projection, cilium membrane
- term:
    id: GO:0005901
    label: caveola
  evidence_type: IDA
  original_reference_id: PMID:11278759
  qualifier: colocalizes_with
  review:
    summary: >-
      The caveola annotation is compatible with a context-specific localization, trafficking state, or
      downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
    reason: >-
      Retained as non-core on the basis of IDA experimental evidence (PMID:11278759); it is secondary
      to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:11278759
      supporting_text: both Smoothened and Patched are in caveolin-1-enriched/raft microdomains.
- term:
    id: GO:0060170
    label: ciliary membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5633040
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The ciliary membrane annotation is
      consistent with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
- term:
    id: GO:0060170
    label: ciliary membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5632668
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The ciliary membrane annotation is
      consistent with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
- term:
    id: GO:0097542
    label: ciliary tip
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5610763
  qualifier: located_in
  review:
    summary: >-
      The ciliary tip annotation is compatible with a context-specific localization, trafficking state,
      or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
    reason: >-
      Retained as non-core on the basis of traceable-author-statement curation (Reactome:R-HSA-5610763);
      it is secondary to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0030666
    label: endocytic vesicle membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5610763
  qualifier: located_in
  review:
    summary: >-
      The endocytic vesicle membrane annotation is compatible with a context-specific localization, trafficking
      state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
    reason: >-
      Retained as non-core on the basis of traceable-author-statement curation (Reactome:R-HSA-5610763);
      it is secondary to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0030666
    label: endocytic vesicle membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5632668
  qualifier: located_in
  review:
    summary: >-
      The endocytic vesicle membrane annotation is compatible with a context-specific localization, trafficking
      state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
    reason: >-
      Retained as non-core on the basis of traceable-author-statement curation (Reactome:R-HSA-5632668);
      it is secondary to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0070062
    label: extracellular exosome
  evidence_type: HDA
  original_reference_id: PMID:23533145
  qualifier: located_in
  review:
    summary: >-
      The extracellular exosome annotation is compatible with a context-specific localization, trafficking
      state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
    reason: >-
      Retained as non-core on the basis of high-throughput direct assay (PMID:23533145); it is secondary
      to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0070062
    label: extracellular exosome
  evidence_type: HDA
  original_reference_id: PMID:19056867
  qualifier: located_in
  review:
    summary: >-
      The extracellular exosome annotation is compatible with a context-specific localization, trafficking
      state, or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
    reason: >-
      Retained as non-core on the basis of high-throughput direct assay (PMID:19056867); it is secondary
      to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005794
    label: Golgi apparatus
  evidence_type: IDA
  original_reference_id: PMID:11278759
  qualifier: colocalizes_with
  review:
    summary: >-
      The Golgi apparatus annotation is compatible with a context-specific localization, trafficking state,
      or downstream role of SMO, but it does not define SMO's core receptor/transducer activity.
    reason: >-
      Retained as non-core on the basis of IDA experimental evidence (PMID:11278759); it is secondary
      to SMO's sterol-regulated signaling activity at the plasma and primary-cilium membranes.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:11278759
      supporting_text: both Smoothened and Patched are in caveolin-1-enriched/raft microdomains.
- term:
    id: GO:0071397
    label: cellular response to cholesterol
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the cellular response to cholesterol; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This curator-reviewed
      orthology transfer is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: file:human/SMO/SMO-uniprot.txt
      supporting_text: G protein-coupled receptor, which transduces the smoothened signaling pathway
- term:
    id: GO:0005929
    label: cilium
  evidence_type: TAS
  original_reference_id: PMID:21931618
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The cilium annotation is consistent
      with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
- term:
    id: GO:0005113
    label: patched binding
  evidence_type: IPI
  original_reference_id: PMID:9811851
  qualifier: enables
  review:
    summary: >-
      Patched proteins negatively regulate SMO and older biochemical experiments reported PTCH-SMO complexes.
      Current mechanistic work emphasizes control of SMO sterol access rather than a required stable receptor
      complex.
    reason: >-
      Retained as non-core because the physical association is reported by PMID:9811851 and supported
      phylogenetically, but patched binding is not the principal molecular activity of SMO.
    action: KEEP_AS_NON_CORE
    supported_by:
    - reference_id: PMID:9811851
      supporting_text: they can form a complex with SMO.
- term:
    id: GO:0007371
    label: ventral midline determination
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      The ventral midline determination annotation records a conserved, context-specific developmental
      output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this
      tissue-level process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible
      and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:2000826
    label: regulation of heart morphogenesis
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      The regulation of heart morphogenesis annotation records a conserved, context-specific developmental
      output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this
      tissue-level process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible
      and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IDA
  original_reference_id: PMID:19304771
  qualifier: located_in
  review:
    summary: >-
      SMO functions as a multi-pass receptor at the plasma membrane and undergoes activation-dependent
      accumulation in the membrane of the non-motile primary cilium. The plasma membrane annotation is
      consistent with this established trafficking and signaling cycle.
    reason: >-
      Accepted as a functionally relevant location. Human cell imaging and biochemical work place SMO
      at the plasma membrane and primary-cilium membrane, where sterol activation and PKA-C regulation
      occur.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19304771
      supporting_text: Binding of two radioligands
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:19304771
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IMP experimental
      evidence is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:19304771
      supporting_text: Binding of two radioligands
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:21177415
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IMP experimental
      evidence is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
- term:
    id: GO:0072285
    label: mesenchymal to epithelial transition involved in metanephric renal vesicle formation
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      The mesenchymal to epithelial transition involved in metanephric renal vesicle formation annotation
      records a conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required
      broadly for morphogen interpretation, but this tissue-level process is not the molecular activity
      that defines the protein.
    reason: >-
      Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible
      and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0090190
    label: positive regulation of branching involved in ureteric bud morphogenesis
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      The positive regulation of branching involved in ureteric bud morphogenesis annotation records a
      conserved, context-specific developmental output of Hedgehog/SMO signaling. SMO is required broadly
      for morphogen interpretation, but this tissue-level process is not the molecular activity that defines
      the protein.
    reason: >-
      Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible
      and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0001947
    label: heart looping
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      The heart looping annotation records a conserved, context-specific developmental output of Hedgehog/SMO
      signaling. SMO is required broadly for morphogen interpretation, but this tissue-level process is
      not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible
      and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0003140
    label: determination of left/right asymmetry in lateral mesoderm
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      The determination of left/right asymmetry in lateral mesoderm annotation records a conserved, context-specific
      developmental output of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation,
      but this tissue-level process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible
      and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: IEP
  original_reference_id: PMID:17850284
  qualifier: involved_in
  review:
    summary: >-
      Expression of SMO in the developing human urogenital sinus is consistent with operation of the
      smoothened signaling pathway during detrusor differentiation. Although IEP is weaker than a functional
      perturbation, the annotated pathway is the core signaling cascade directly transduced by SMO.
    reason: >-
      Accepted for consistency with the extensive direct biochemical and genetic evidence that SMO transduces
      this pathway. PMID:17850284 provides human developmental expression context rather than the sole basis
      for the mechanistic assignment.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:17850284
      supporting_text: >-
        The expression patterns of the SHH-transducing proteins Patched (PTCH) and Smoothened (SMO) were
        consistent with long-range paracrine signalling associated with detrusor smooth muscle differentiation
        in the urogenital sinus.
- term:
    id: GO:0007494
    label: midgut development
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      The midgut development annotation records a conserved, context-specific developmental output of
      Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level
      process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible
      and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0048853
    label: forebrain morphogenesis
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      The forebrain morphogenesis annotation records a conserved, context-specific developmental output
      of Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level
      process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible
      and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0061053
    label: somite development
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: involved_in
  review:
    summary: >-
      The somite development annotation records a conserved, context-specific developmental output of
      Hedgehog/SMO signaling. SMO is required broadly for morphogen interpretation, but this tissue-level
      process is not the molecular activity that defines the protein.
    reason: >-
      Retained as non-core. The curator-reviewed orthology transfer (GO_REF:0000024) is biologically plausible
      and consistent with SMO's pleiotropic developmental role, while the core function remains sterol-regulated
      ciliary signal transduction.
    action: KEEP_AS_NON_CORE
- term:
    id: GO:0007224
    label: smoothened signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:9422511
  qualifier: involved_in
  review:
    summary: >-
      SMO is the membrane transducer of the smoothened signaling pathway; activation by sterols couples
      SMO to Gi and/or direct PKA-C inhibition and thereby permits GLI activation. This IMP experimental
      evidence is mechanistically concordant with direct human SMO studies.
    reason: >-
      Accepted as a core process annotation. The annotation names the signaling cascade or an immediate
      biochemical branch in which SMO directly acts, rather than a remote developmental phenotype.
    action: ACCEPT
    supported_by:
    - reference_id: PMID:9422511
      supporting_text: These findings support the role of SMO as a signalling component of the SHH-receptor
        complex
- term:
    id: GO:0060242
    label: contact inhibition
  evidence_type: IMP
  original_reference_id: PMID:9422511
  qualifier: involved_in
  review:
    summary: >-
      The cited experimental annotation may be valid, but the cached publication record does not expose
      enough assay detail to verify the exact contact inhibition claim for human SMO.
    reason: >-
      Undecided because the relevant full text is unavailable locally. In accordance with the project
      policy, the experimental curator is not overruled from title/abstract-level evidence alone.
    action: UNDECIDED
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19592253
  qualifier: enables
  review:
    summary: >-
      The cited experimental annotation may be valid, but the cached publication record does not expose
      enough assay detail to verify the exact protein binding claim for human SMO.
    reason: >-
      Undecided because the relevant full text is unavailable locally. In accordance with the project
      policy, the experimental curator is not overruled from title/abstract-level evidence alone.
    action: UNDECIDED
- term:
    id: GO:0004862
    label: cAMP-dependent protein kinase inhibitor activity
  evidence_type: IDA
  original_reference_id: PMID:36202993
  qualifier: enables
  review:
    summary: >-
      SMO contains a C-terminal PKI pseudosubstrate motif that directly occupies the PKA catalytic-subunit
      active site and inhibits its kinase activity, preventing inhibitory GLI phosphorylation.
    action: NEW
    reason: >-
      Proposed because this specific molecular function is directly demonstrated in biochemical, cellular,
      and organismal assays in PMID:36202993 and is more informative than generic protein sequestering
      activity or PKA catalytic-subunit binding.
    additional_reference_ids:
    - PMID:39138140
    supported_by:
    - reference_id: PMID:36202993
      supporting_text: >-
        SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent
        protein kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity.
    - reference_id: PMID:39138140
      supporting_text: GRK2 phosphorylation enables active SMO to bind PKA-C directly.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000024
  title: >-
    Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment
    of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: >-
    Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied
    by conservative changes to GO terms applied by UniProt
  findings: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000107
  title: >-
    Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl
    Compara
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:11278759
  title: >-
    The sonic hedgehog receptor patched associates with caveolin-1 in cholesterol-rich microdomains of
    the plasma membrane.
  findings: []
- id: PMID:17850284
  title: Immunohistochemical analysis of Sonic hedgehog signalling in normal human urinary tract development.
  findings: []
- id: PMID:19056867
  title: Large-scale proteomics and phosphoproteomics of urinary exosomes.
  findings: []
- id: PMID:19304771
  title: Evidence for allosteric interactions of antagonist binding to the smoothened receptor.
  findings: []
- id: PMID:19592253
  title: >-
    The mammalian Cos2 homolog Kif7 plays an essential role in modulating Hh signal transduction during
    development.
  findings: []
- id: PMID:21177415
  title: >-
    Identification and mechanism of action of the acylguanidine MRT-83, a novel potent Smoothened antagonist.
  findings: []
- id: PMID:21659505
  title: >-
    Growth Arrest Specific 8 (Gas8) and G protein-coupled receptor kinase 2 (GRK2) cooperate in the control
    of Smoothened signaling.
  findings: []
- id: PMID:21671467
  title: miR-338-3p suppresses invasion of liver cancer cell by targeting smoothened.
  findings: []
- id: PMID:21931618
  title: The hedgehog receptor patched is involved in cholesterol transport.
  findings: []
- id: PMID:22072986
  title: A novel protein LZTFL1 regulates ciliary trafficking of the BBSome and Smoothened.
  findings:
  - statement: >-
      Endogenous SMO accumulates in primary cilia in response to agonist, with BBSome/LZTFL1 controlling
      its ciliary trafficking.
    supporting_text: >-
      In control siRNA transfected cells, SMO localizes to the cilia in response to SMO agonist (SAG)
      but not in SAG-untreated cells
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Full text read from PMC3207910; directly supports ciliary localization and regulated SMO trafficking
      in human RPE1 cells.
- id: PMID:23533145
  title: In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine.
  findings: []
- id: PMID:27437577
  title: Structural basis of Smoothened regulation by its extracellular domains.
  findings:
  - statement: >-
      Human SMO contains a cholesterol-binding site in its extracellular cysteine-rich domain, and mutations
      that disrupt cholesterol binding impair native Hedgehog signal transmission.
    supporting_text: Unexpectedly, we find a cholesterol molecule bound to Smoothened in the CRD binding
      site.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Full text read from PMC4970916; directly establishes cholesterol binding and its functional importance
      for SMO signaling.
- id: PMID:27727273
  title: Zfp423 Regulates Sonic Hedgehog Signaling via Primary Cilium Function.
  findings: []
- id: PMID:31168089
  title: Cryo-EM structure of oxysterol-bound human Smoothened coupled to a heterotrimeric G(i).
  findings:
  - statement: >-
      Oxysterol-bound human SMO directly couples to heterotrimeric Gi and activates Gi-dependent Hedgehog
      signaling.
    supporting_text: >-
      We present a cryo-electron microscopy structure of human SMO bound to 24(S),25-epoxycholesterol
      and coupled to a heterotrimeric Gi protein.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Full text read from PMC6777001; directly supports class-F GPCR activity, oxysterol responsiveness,
      Gi coupling, and Hedgehog transduction.
- id: PMID:32413283
  title: >-
    Bi-allelic Variations of SMO in Humans Cause a Broad Spectrum of Developmental Anomalies Due to Abnormal
    Hedgehog Signaling.
  findings:
  - statement: >-
      Biallelic human SMO loss-of-function variants disrupt primary-cilium pathway dynamics and cause
      multisystem developmental anomalies.
    supporting_text: >-
      Cells derived from affected individuals showed normal ciliogenesis but severely altered Hh-signal
      transduction as a result of either altered PC trafficking or abnormal activation of the pathway
      downstream of SMO.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed identifier and abstract verified; cache is abstract-only, so only abstract-supported human
      genetic and cellular claims were used.
- id: PMID:32929279
  title: Sterols in an intramolecular channel of Smoothened mediate Hedgehog signaling.
  findings:
  - statement: Sterols occupy connected binding sites within SMO and regulate its active signaling conformation.
    supporting_text: >-
      These data indicate that sterol transport through the core of SMO is a major regulator of SMO-mediated
      signaling.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Full text read from PMC7669734; directly supports sterol binding and sterol-controlled SMO signaling.
- id: PMID:36202993
  title: A PKA inhibitor motif within SMOOTHENED controls Hedgehog signal transduction.
  findings:
  - statement: >-
      The SMO PKI pseudosubstrate motif directly inhibits PKA catalytic activity and is required for Hedgehog
      signal transduction.
    supporting_text: >-
      SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein
      kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Full text read from PMC9696579; establishes the direct PKA-inhibitor mechanism and supports the
      proposed specific MF annotation.
- id: PMID:39138140
  title: GRK2 kinases in the primary cilium initiate SMOOTHENED-PKA signaling in the Hedgehog cascade.
  findings:
  - statement: >-
      GRK2 phosphorylation of active ciliary SMO triggers direct PKA-C binding and inactivation during
      endogenous Hedgehog signaling.
    supporting_text: GRK2 phosphorylation enables active SMO to bind PKA-C directly.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Full text read from PMC11322411; validates the ciliary SMO-GRK2-PKA mechanism across cellular and
      in vivo models.
- id: PMID:9422511
  title: Activating Smoothened mutations in sporadic basal-cell carcinoma.
  findings:
  - statement: Activating human SMO mutations drive Hedgehog-pathway signaling and oncogenic transformation.
    supporting_text: These findings support the role of SMO as a signalling component of the SHH-receptor
      complex
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      PubMed identifier and abstract verified. The cache is abstract-only; the pathway annotation is supported,
      while the exact contact-inhibition assay was left undecided.
- id: PMID:9811851
  title: Characterization of two patched receptors for the vertebrate hedgehog protein family.
  findings:
  - statement: Biochemical analysis reported that PTCH1 and PTCH2 can form complexes with SMO.
    supporting_text: they can form a complex with SMO.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: >-
      PubMed identifier and abstract verified. Supports the historical patched-binding annotation, retained
      as non-core because modern sterol-access models do not require a stable complex.
- id: Reactome:R-HSA-5610763
  title: PTCH1 inhibits accumulation of SMO in the primary cilium in the absence of Hh signal
  findings: []
- id: Reactome:R-HSA-5632668
  title: SMO translocates to the cilium
  findings: []
- id: Reactome:R-HSA-5633040
  title: CSNK1A1 and ADRBK1 dissociate from p-SMO dimer
  findings: []
- id: file:human/SMO/SMO-uniprot.txt
  title: UniProtKB reviewed record for human SMO (Q99835)
  findings:
  - statement: >-
      SMO is a sterol-activated GPCR that signals through Gi and direct PKA-C sequestration at plasma
      and ciliary membranes.
    supporting_text: G protein-coupled receptor, which transduces the smoothened signaling pathway
    reference_section_type: DATABASE_ENTRY
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Reviewed UniProtKB/Swiss-Prot record Q99835 inspected locally; its mechanistic statements are anchored
      to the primary publications also reviewed here.
core_functions:
- description: >-
    Sterol-regulated class-F G protein-coupled receptor activity that transduces Hedgehog input across
    the plasma and primary-cilium membranes. Active SMO couples to heterotrimeric Gi, lowering cellular
    cAMP, and promotes GLI activation.
  molecular_function:
    id: GO:0004930
    label: G protein-coupled receptor activity
  directly_involved_in:
  - id: GO:0007224
    label: smoothened signaling pathway
  - id: GO:0007193
    label: adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
  locations:
  - id: GO:0005886
    label: plasma membrane
  - id: GO:0098804
    label: non-motile cilium membrane
  supported_by:
  - reference_id: PMID:31168089
    supporting_text: >-
      We present a cryo-electron microscopy structure of human SMO bound to 24(S),25-epoxycholesterol
      and coupled to a heterotrimeric Gi protein.
  - reference_id: PMID:32929279
    supporting_text: >-
      Smoothened (SMO), a class Frizzled G protein-coupled receptor (class F GPCR), transduces the Hedgehog
      signal across the cell membrane.
- description: >-
    Cholesterol/sterol binding through the extracellular cysteine-rich domain and connected transmembrane
    sites; ligand occupancy and sterol movement stabilize signaling-competent SMO conformations required
    for native Hedgehog responses.
  molecular_function:
    id: GO:0015485
    label: cholesterol binding
  directly_involved_in:
  - id: GO:0007224
    label: smoothened signaling pathway
  locations:
  - id: GO:0005886
    label: plasma membrane
  - id: GO:0098804
    label: non-motile cilium membrane
  supported_by:
  - reference_id: PMID:27437577
    supporting_text: Unexpectedly, we find a cholesterol molecule bound to Smoothened in the CRD binding
      site.
  - reference_id: PMID:32929279
    supporting_text: >-
      These data indicate that sterol transport through the core of SMO is a major regulator of SMO-mediated
      signaling.
- description: >-
    Direct cAMP-dependent protein kinase inhibitor activity: the phosphorylated C-terminal SMO PKI motif
    acts as a pseudosubstrate that binds the PKA catalytic-subunit active site, sequesters and inhibits
    PKA-C, and thereby prevents inhibitory GLI phosphorylation during Hedgehog signaling.
  molecular_function:
    id: GO:0004862
    label: cAMP-dependent protein kinase inhibitor activity
  directly_involved_in:
  - id: GO:0007224
    label: smoothened signaling pathway
  locations:
  - id: GO:0098804
    label: non-motile cilium membrane
  supported_by:
  - reference_id: PMID:36202993
    supporting_text: >-
      SMO uses a decoy substrate sequence to physically block the active site of the cAMP-dependent protein
      kinase (PKA) catalytic subunit (PKA-C) and extinguish its enzymatic activity.
  - reference_id: PMID:39138140
    supporting_text: GRK2 phosphorylation enables active SMO to bind PKA-C directly.
proposed_new_terms: []
suggested_questions:
- question: >-
    In which human cell types does SMO signal predominantly through heterotrimeric Gi versus direct PKA-C
    inhibition, and how are these two immediate effector routes integrated?
- question: >-
    Which endogenous cholesterol or oxysterol species occupies each SMO sterol-binding site in specific
    physiological tissues?
suggested_experiments:
- hypothesis: >-
    Gi coupling and PKI-motif-dependent PKA inhibition make separable, cell-context-dependent contributions
    to human SMO-to-GLI signaling.
  description: >-
    Introduce endogenous separation-of-function SMO alleles that selectively disrupt Gi coupling or the
    PKI pseudosubstrate motif in human ciliated neural and mesenchymal organoids. Measure ciliary SMO
    trafficking, local and whole-cell cAMP, PKA substrate phosphorylation, GLI processing, and GLI target
    transcription after defined SHH and sterol stimulation, with wild-type rescue controls.
  experiment_type: CRISPR knock-in with live-cell signaling and organoid phenotyping