SC5D encodes lathosterol oxidase (sterol-C5-desaturase / delta7-sterol 5(6)-desaturase; EC 1.14.19.20), a non-heme di-iron oxidoreductase of the sterol desaturase family that is anchored as a multi-pass protein in the endoplasmic reticulum membrane. It introduces the C5-6 double bond into lathosterol, converting it to 7-dehydrocholesterol (7-DHC) using molecular oxygen and electrons delivered from cytochrome b5. This is the penultimate step of cholesterol biosynthesis (the Kandutsch-Russell arm), immediately upstream of DHCR7, which reduces 7-DHC to cholesterol; the enzyme can act on additional Delta(7)-sterols such as 5alpha-cholesta-7,24-dien-3beta-ol in the Bloch arm. The three conserved histidine-box motifs coordinate the di-iron center that constitutes the active site. Loss-of-function variants cause lathosterolosis, an autosomal recessive disorder with elevated lathosterol and a Smith-Lemli-Opitz-like multiple-malformation / dysmorphism phenotype with liver disease and lysosomal storage; the mouse knockout is perinatal-lethal with craniofacial and limb patterning defects consistent with impaired hedgehog signalling from cholesterol deficiency. Because its product 7-DHC is a highly reactive radical-trapping sterol, SC5D also indirectly modulates ferroptosis sensitivity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005789
endoplasmic reticulum membrane
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) inference that SC5D acts in the endoplasmic reticulum membrane. This matches the experimentally determined subcellular location and the multi-pass membrane topology predicted from the sequence.
Reason: SC5D is a sterol desaturase-family enzyme of cholesterol biosynthesis, a pathway localized to the ER membrane; the human protein was shown to be an integral ER membrane protein experimentally (PMID:10786622).
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Endoplasmic reticulum membrane
|
|
GO:0050046
delta7-sterol 5(6)-desaturase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) inference of the precise catalytic activity: SC5D introduces the C5(6) double bond into Delta(7)-sterols. This is the enzyme's core molecular function and is confirmed experimentally.
Reason: Directly supported by cloning/complementation and by the UniProt CATALYTIC ACTIVITY (RHEA:54320/46556; EC 1.14.19.20). Represents the core MF of the gene.
Supporting Evidence:
PMID:10786622
introduce C5-6 double bond into lathosterol in cholesterol biosynthesis
|
|
GO:0000248
C-5 sterol desaturase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic (IBA) inference of C-5 sterol desaturase activity, the more general parent of the specific Delta(7)-sterol 5(6)-desaturase reaction. Correct family-level molecular function.
Reason: Consistent with the sterol desaturase family assignment and experimental characterization; a valid, if slightly more general, statement of the core catalytic function.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Belongs to the sterol desaturase family
|
|
GO:0005506
iron ion binding
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: InterPro2GO inference of iron ion binding. SC5D is a non-heme di-iron sterol desaturase whose three conserved histidine-box motifs coordinate the catalytic iron center; UniProt lists an Fe cation cofactor.
Reason: Well-supported for this enzyme family: the His-box motifs (138-143, 151-155, 228-233) form the metal-binding active site and the cofactor is an Fe cation, so iron ion binding is an accurate molecular function.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Name=Fe cation
file:human/SC5D/SC5D-uniprot.txt
The histidine box domains may contain the active site
|
|
GO:0005789
endoplasmic reticulum membrane
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic (UniProt/rat-ortholog) transfer of ER membrane localization. Redundant with the experimental IDA and IBA ER-membrane annotations and consistent with the multi-pass membrane topology.
Reason: Correct localization, independently supported by the human IDA (PMID:10786622) and by the predicted transmembrane helices.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Endoplasmic reticulum membrane
|
|
GO:0008610
lipid biosynthetic process
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: InterPro2GO inference of the broad process "lipid biosynthetic process". SC5D acts in cholesterol (a sterol lipid) biosynthesis, so this is correct but general relative to the specific cholesterol/sterol biosynthesis terms also annotated.
Reason: Not wrong: cholesterol biosynthesis is-a lipid biosynthetic process. It is a broad parent, but per curation guidance broad correct IEA parents can be accepted; the more specific term (GO:0006695) captures the core process.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Steroid biosynthesis; cholesterol biosynthesis
|
|
GO:0050046
delta7-sterol 5(6)-desaturase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic (UniProt, via rat ortholog and RHEA/EC mapping) transfer of the precise Delta(7)-sterol 5(6)-desaturase activity. Redundant with the IBA and IDA/EXP annotations of the same activity.
Reason: Correct core catalytic function backed by the RHEA reactions and EC 1.14.19.20 in the UniProt record.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
EC=1.14.19.20
|
|
GO:0000248
C-5 sterol desaturase activity
|
IEA
GO_REF:0000107 |
ACCEPT |
Summary: Ensembl-Compara ortholog transfer (from rat) of C-5 sterol desaturase activity. Consistent with the experimental and phylogenetic annotations of the same family-level function.
Reason: Accurate family-level molecular function; redundant with the IBA/EXP annotations of GO:0000248.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Belongs to the sterol desaturase family
|
|
GO:0006695
cholesterol biosynthetic process
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic (UniProt/UniPathway) transfer of cholesterol biosynthetic process. SC5D catalyzes the penultimate step of cholesterol biosynthesis, so this is the correct core biological process.
Reason: Directly matches the enzyme's role and the UniProt PATHWAY statement; independently supported by human IDA and disease evidence.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Steroid biosynthesis; cholesterol biosynthesis
|
|
GO:0006695
cholesterol biosynthetic process
|
TAS
Reactome:R-HSA-6807047 |
ACCEPT |
Summary: Reactome (TAS) placement of SC5D in cholesterol biosynthesis via the desmosterol/Bloch pathway. Correct: SC5D also desaturates the Bloch-arm intermediate 5alpha-cholesta-7,24-dien-3beta-ol.
Reason: SC5D participates in both the Bloch and Kandutsch-Russell arms; its Delta(7)-sterol 5(6)-desaturase activity applies to the corresponding Bloch intermediate. Core biological process.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Steroid biosynthesis; cholesterol biosynthesis
|
|
GO:0006695
cholesterol biosynthetic process
|
TAS
Reactome:R-HSA-9969901 |
ACCEPT |
Summary: Reactome (TAS) placement of SC5D in cholesterol biosynthesis from zymosterol (modified Kandutsch-Russell pathway), the lathosterol arm in which SC5D acts. Correct core biological process.
Reason: This is the canonical arm containing the SC5D-catalyzed lathosterol -> 7-dehydrocholesterol step; well supported.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Catalyzes the penultimate step
|
|
GO:0050046
delta7-sterol 5(6)-desaturase activity
|
EXP
PMID:38297129 7-Dehydrocholesterol is an endogenous suppressor of ferropto... |
ACCEPT |
Summary: Experimental (EXP) annotation of Delta(7)-sterol 5(6)-desaturase activity from the Nature ferroptosis study, which characterized SC5D FUNCTION and CATALYTIC ACTIVITY as the enzyme producing 7-DHC. Confirms the core catalytic function.
Reason: Experimental support for the precise reaction; underpins the UniProt CATALYTIC ACTIVITY entries. Core molecular function.
Supporting Evidence:
PMID:38297129
an unexpected prosurvival
file:human/SC5D/SC5D-uniprot.txt
Catalyzes the penultimate step
|
|
GO:0005789
endoplasmic reticulum membrane
|
IDA
PMID:10786622 cDNA cloning of the mammalian sterol C5-desaturase and the e... |
ACCEPT |
Summary: Experimental (IDA) determination that SC5D is an integral endoplasmic reticulum membrane protein, from the cloning study that also demonstrated the enzymatic activity by yeast-mutant complementation.
Reason: Primary experimental evidence for the ER-membrane location; the core cellular component for this enzyme.
Supporting Evidence:
PMID:10786622
Mammalian SC5D was presumed as an integral
file:human/SC5D/SC5D-uniprot.txt
Endoplasmic reticulum membrane
|
|
GO:0006695
cholesterol biosynthetic process
|
IDA
PMID:10786622 cDNA cloning of the mammalian sterol C5-desaturase and the e... |
ACCEPT |
Summary: Experimental (IDA) annotation to cholesterol biosynthetic process from the cloning/complementation study, which functionally showed SC5D introduces the C5-6 double bond into lathosterol in cholesterol biosynthesis. This is the correct core biological process.
Reason: Direct experimental support for SC5D's role in cholesterol biosynthesis. A more specific child term (GO:0033490, cholesterol biosynthetic process via lathosterol) is proposed separately as a NEW annotation to capture the precise lathosterol arm.
Supporting Evidence:
PMID:10786622
introduce C5-6 double bond into lathosterol in cholesterol biosynthesis
|
|
GO:0033490
cholesterol biosynthetic process via lathosterol
|
IDA
PMID:10786622 cDNA cloning of the mammalian sterol C5-desaturase and the e... |
NEW |
Summary: Proposed more specific annotation: SC5D acts in the lathosterol arm of cholesterol biosynthesis, catalyzing lathosterol -> 7-dehydrocholesterol. UniProt assigns this precise child term (GO:0033490, IDA:UniProtKB); it is not yet in GOA and is added here as a NEW, more informative annotation.
Reason: Sharper than the generic GO:0006695: the lathosterol-specific arm is the exact pathway context of the SC5D reaction, matching the UniProt IDA annotation.
Supporting Evidence:
PMID:10786622
introduce C5-6 double bond into lathosterol in cholesterol biosynthesis
|
|
GO:0050046
delta7-sterol 5(6)-desaturase activity
|
IDA
PMID:10786622 cDNA cloning of the mammalian sterol C5-desaturase and the e... |
ACCEPT |
Summary: Experimental (IDA) annotation of Delta(7)-sterol 5(6)-desaturase activity. The human cDNA functionally complemented a sterol-C5-desaturase-defective yeast mutant, directly demonstrating the catalytic activity.
Reason: Direct experimental demonstration of the core catalytic function via yeast complementation.
Supporting Evidence:
PMID:10786622
functional complementation of a defective yeast mutant proves that the human and
|
|
GO:0110076
negative regulation of ferroptosis
|
IMP
PMID:38297129 7-Dehydrocholesterol is an endogenous suppressor of ferropto... |
KEEP AS NON CORE |
Summary: Loss-of-function (IMP) evidence that SC5D negatively regulates ferroptosis. As a distal-cholesterol-biosynthesis enzyme, SC5D produces 7-DHC, a potent radical-trapping sterol that shields (phospho)lipids from autoxidation; loss of SC5D lowers 7-DHC and sensitizes cells to ferroptosis. This is a real but indirect, non-core role mediated by the 7-DHC product.
Reason: Supported experimentally, but the effect is a downstream/indirect consequence of SC5D's catalytic product (7-DHC) rather than a distinct molecular activity of SC5D itself; the core function is C5-sterol desaturation in cholesterol biosynthesis. Keep as a non-core process.
Supporting Evidence:
PMID:38297129
we now show that 7-DHC accumulation
|
|
GO:0110076
negative regulation of ferroptosis
|
IMP
PMID:38297130 7-Dehydrocholesterol dictates ferroptosis sensitivity. |
KEEP AS NON CORE |
Summary: Loss-of-function (IMP) evidence from a genome-wide CRISPR screen: SC5D is an anti-ferroptotic distal-cholesterol-biosynthesis gene. SC5D knockout increased ferroptosis susceptibility and lowered 7-DHC, and re-expression rescued the phenotype. Indirect, non-core role via the 7-DHC product.
Reason: Well supported experimentally in this full-text study, but mechanistically the protection is conferred by the SC5D reaction product 7-DHC, not by an independent SC5D activity; keep as a non-core biological process.
Supporting Evidence:
PMID:38297130
individual deletion of CYP51A1, MSMO1, EBP and SC5D in HEK293T cells increased the susceptibility to ferroptosis
PMID:38297130
Re-expression of SC5D reversed the severity of ferroptosis induced by RSL3 in SC5D KO cells
|
|
GO:0000248
C-5 sterol desaturase activity
|
EXP
PMID:12189593 Lathosterolosis, a novel multiple-malformation/mental retard... |
ACCEPT |
Summary: Experimental (EXP) annotation of C-5 sterol desaturase activity based on the first human lathosterolosis patient, in whom the SC5D-catalyzed conversion of lathosterol to 7-dehydrocholesterol was blocked and the enzyme activity was deficient. Supports the core catalytic function.
Reason: Human patient data directly link SC5D to C-5 sterol desaturase activity (loss of activity blocks lathosterol -> 7-DHC). Core molecular function.
Supporting Evidence:
PMID:12189593
showing a block in the conversion of lathosterol into
PMID:12189593
was deficient in the patient's
|
|
GO:0000248
C-5 sterol desaturase activity
|
EXP
PMID:12812989 Lathosterolosis: an inborn error of human and murine cholest... |
ACCEPT |
Summary: Experimental (EXP) annotation of C-5 sterol desaturase activity supported by the human patient and Sc5d-null mouse study, which established that lathosterol 5-desaturase catalyzes the conversion of lathosterol to 7-dehydrocholesterol in the next-to-last step of cholesterol synthesis.
Reason: Combined human and mouse loss-of-function evidence for the core catalytic function; elevated lathosterol and decreased cholesterol on enzyme loss.
Supporting Evidence:
PMID:12812989
catalyzes the conversion of lathosterol to
PMID:12812989
had elevated lathosterol and decreased cholesterol
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-1655852 |
ACCEPT |
Summary: Reactome (TAS) ER-membrane localization associated with expression of lathosterol oxidase (SC5D). Consistent with the experimental IDA and the multi-pass membrane topology.
Reason: Redundant with the experimentally determined ER membrane location; correct core cellular component.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Endoplasmic reticulum membrane
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-195664 |
ACCEPT |
Summary: Reactome (TAS) ER-membrane localization for the SC5D-catalyzed desaturation of cholesta-7,24-dien-3beta-ol (a Bloch-arm reaction). Consistent with the established ER location.
Reason: Correct core cellular component; the reaction it is attached to takes place in the ER, as noted by Reactome, and matches the human IDA.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Endoplasmic reticulum membrane
|
|
GO:0005789
endoplasmic reticulum membrane
|
TAS
Reactome:R-HSA-6807053 |
ACCEPT |
Summary: Reactome (TAS) ER-membrane localization for the SC5D reaction that desaturates lathosterol to 7-dehydrocholesterol. Consistent with the experimental and predicted ER-membrane location.
Reason: Correct core cellular component; matches human IDA and topology.
Supporting Evidence:
file:human/SC5D/SC5D-uniprot.txt
Endoplasmic reticulum membrane
|
Q: Is SC5D's role in modulating ferroptosis (via 7-DHC) physiologically relevant in normal tissues, or primarily a cancer-context phenomenon?
Q: To what extent does SC5D contribute to the Bloch versus Kandutsch-Russell arms of cholesterol biosynthesis in different human tissues?
Experiment: Reconstitute purified human SC5D with cytochrome b5 / cytochrome b5 reductase to measure the di-iron-dependent desaturation kinetics on lathosterol versus 5alpha-cholesta-7,24-dien-3beta-ol and confirm cofactor stoichiometry.
Hypothesis: SC5D is a non-heme di-iron desaturase that uses electrons from cytochrome b5 to desaturate multiple Delta(7)-sterol substrates.
Experiment: Site-directed mutagenesis of the three histidine-box motifs to test their requirement for iron binding and catalysis, complementing the disease-variant (R29Q, Y46S, G211D) structure-function analysis.
Hypothesis: The conserved histidine-box motifs coordinate the catalytic di-iron center and are essential for C5-sterol desaturase activity.
UniProtKB: O75845 (SC5D_HUMAN), 299 aa. HGNC:10547. EC 1.14.19.20.
SC5D is lathosterol oxidase / sterol-C5(6)-desaturase, a non-heme-iron,
multi-pass endoplasmic-reticulum-membrane oxidoreductase that introduces the
C5β6 double bond into lathosterol, producing 7-dehydrocholesterol (7-DHC). This
is the penultimate step of cholesterol biosynthesis (KandutschβRussell arm),
immediately upstream of DHCR7 which reduces 7-DHC to cholesterol.
lathosterol + 2 Fe(II)-[cyt b5] + O2 + 2 H+ = 7-dehydrocholesterol + 2 Fe(III)-[cyt b5] + 2 H2O (RHEA:46556; EC 1.14.19.20).
Also acts on 5Ξ±-cholesta-7,24-dien-3Ξ²-ol β 7-dehydrodesmosterol (RHEA:47184; Bloch-arm intermediate).
Lathosterolosis (LATHOS, MIM:607330): autosomal recessive; elevated lathosterol;
SLOS-like multiple-malformation / dysmorphism syndrome with liver disease and
lysosomal storage. Caused by SC5D variants.
id: O75845
gene_symbol: SC5D
product_type: PROTEIN
status: INITIALIZED
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
SC5D encodes lathosterol oxidase (sterol-C5-desaturase / delta7-sterol
5(6)-desaturase; EC 1.14.19.20), a non-heme di-iron oxidoreductase of the
sterol desaturase family that is anchored as a multi-pass protein in the
endoplasmic reticulum membrane. It introduces the C5-6 double bond into
lathosterol, converting it to 7-dehydrocholesterol (7-DHC) using molecular
oxygen and electrons delivered from cytochrome b5. This is the penultimate
step of cholesterol biosynthesis (the Kandutsch-Russell arm), immediately
upstream of DHCR7, which reduces 7-DHC to cholesterol; the enzyme can act on
additional Delta(7)-sterols such as 5alpha-cholesta-7,24-dien-3beta-ol in the
Bloch arm. The three conserved histidine-box motifs coordinate the di-iron
center that constitutes the active site. Loss-of-function variants cause
lathosterolosis, an autosomal recessive disorder with elevated lathosterol and
a Smith-Lemli-Opitz-like multiple-malformation / dysmorphism phenotype with
liver disease and lysosomal storage; the mouse knockout is perinatal-lethal
with craniofacial and limb patterning defects consistent with impaired
hedgehog signalling from cholesterol deficiency. Because its product 7-DHC is
a highly reactive radical-trapping sterol, SC5D also indirectly modulates
ferroptosis sensitivity.
existing_annotations:
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: is_active_in
review:
summary: >-
Phylogenetic (IBA) inference that SC5D acts in the endoplasmic reticulum
membrane. This matches the experimentally determined subcellular location
and the multi-pass membrane topology predicted from the sequence.
action: ACCEPT
reason: >-
SC5D is a sterol desaturase-family enzyme of cholesterol biosynthesis, a
pathway localized to the ER membrane; the human protein was shown to be an
integral ER membrane protein experimentally (PMID:10786622).
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Endoplasmic reticulum membrane"
- term:
id: GO:0050046
label: delta7-sterol 5(6)-desaturase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: >-
Phylogenetic (IBA) inference of the precise catalytic activity: SC5D
introduces the C5(6) double bond into Delta(7)-sterols. This is the
enzyme's core molecular function and is confirmed experimentally.
action: ACCEPT
reason: >-
Directly supported by cloning/complementation and by the UniProt
CATALYTIC ACTIVITY (RHEA:54320/46556; EC 1.14.19.20). Represents the core
MF of the gene.
supported_by:
- reference_id: PMID:10786622
supporting_text: "introduce C5-6 double bond into lathosterol in cholesterol biosynthesis"
- term:
id: GO:0000248
label: C-5 sterol desaturase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: >-
Phylogenetic (IBA) inference of C-5 sterol desaturase activity, the
more general parent of the specific Delta(7)-sterol 5(6)-desaturase
reaction. Correct family-level molecular function.
action: ACCEPT
reason: >-
Consistent with the sterol desaturase family assignment and experimental
characterization; a valid, if slightly more general, statement of the
core catalytic function.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Belongs to the sterol desaturase family"
- term:
id: GO:0005506
label: iron ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: >-
InterPro2GO inference of iron ion binding. SC5D is a non-heme di-iron
sterol desaturase whose three conserved histidine-box motifs coordinate
the catalytic iron center; UniProt lists an Fe cation cofactor.
action: ACCEPT
reason: >-
Well-supported for this enzyme family: the His-box motifs (138-143,
151-155, 228-233) form the metal-binding active site and the cofactor is
an Fe cation, so iron ion binding is an accurate molecular function.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Name=Fe cation"
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "The histidine box domains may contain the active site"
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: located_in
review:
summary: >-
Electronic (UniProt/rat-ortholog) transfer of ER membrane localization.
Redundant with the experimental IDA and IBA ER-membrane annotations and
consistent with the multi-pass membrane topology.
action: ACCEPT
reason: >-
Correct localization, independently supported by the human IDA
(PMID:10786622) and by the predicted transmembrane helices.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Endoplasmic reticulum membrane"
- term:
id: GO:0008610
label: lipid biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: >-
InterPro2GO inference of the broad process "lipid biosynthetic process".
SC5D acts in cholesterol (a sterol lipid) biosynthesis, so this is correct
but general relative to the specific cholesterol/sterol biosynthesis
terms also annotated.
action: ACCEPT
reason: >-
Not wrong: cholesterol biosynthesis is-a lipid biosynthetic process. It is
a broad parent, but per curation guidance broad correct IEA parents can be
accepted; the more specific term (GO:0006695) captures the core process.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Steroid biosynthesis; cholesterol biosynthesis"
- term:
id: GO:0050046
label: delta7-sterol 5(6)-desaturase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: >-
Electronic (UniProt, via rat ortholog and RHEA/EC mapping) transfer of the
precise Delta(7)-sterol 5(6)-desaturase activity. Redundant with the IBA
and IDA/EXP annotations of the same activity.
action: ACCEPT
reason: >-
Correct core catalytic function backed by the RHEA reactions and EC
1.14.19.20 in the UniProt record.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "EC=1.14.19.20"
- term:
id: GO:0000248
label: C-5 sterol desaturase activity
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: enables
review:
summary: >-
Ensembl-Compara ortholog transfer (from rat) of C-5 sterol desaturase
activity. Consistent with the experimental and phylogenetic annotations of
the same family-level function.
action: ACCEPT
reason: >-
Accurate family-level molecular function; redundant with the IBA/EXP
annotations of GO:0000248.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Belongs to the sterol desaturase family"
- term:
id: GO:0006695
label: cholesterol biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: involved_in
review:
summary: >-
Electronic (UniProt/UniPathway) transfer of cholesterol biosynthetic
process. SC5D catalyzes the penultimate step of cholesterol biosynthesis,
so this is the correct core biological process.
action: ACCEPT
reason: >-
Directly matches the enzyme's role and the UniProt PATHWAY statement;
independently supported by human IDA and disease evidence.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Steroid biosynthesis; cholesterol biosynthesis"
- term:
id: GO:0006695
label: cholesterol biosynthetic process
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6807047
qualifier: involved_in
review:
summary: >-
Reactome (TAS) placement of SC5D in cholesterol biosynthesis via the
desmosterol/Bloch pathway. Correct: SC5D also desaturates the Bloch-arm
intermediate 5alpha-cholesta-7,24-dien-3beta-ol.
action: ACCEPT
reason: >-
SC5D participates in both the Bloch and Kandutsch-Russell arms; its
Delta(7)-sterol 5(6)-desaturase activity applies to the corresponding
Bloch intermediate. Core biological process.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Steroid biosynthesis; cholesterol biosynthesis"
- term:
id: GO:0006695
label: cholesterol biosynthetic process
evidence_type: TAS
original_reference_id: Reactome:R-HSA-9969901
qualifier: involved_in
review:
summary: >-
Reactome (TAS) placement of SC5D in cholesterol biosynthesis from
zymosterol (modified Kandutsch-Russell pathway), the lathosterol arm in
which SC5D acts. Correct core biological process.
action: ACCEPT
reason: >-
This is the canonical arm containing the SC5D-catalyzed lathosterol ->
7-dehydrocholesterol step; well supported.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Catalyzes the penultimate step"
- term:
id: GO:0050046
label: delta7-sterol 5(6)-desaturase activity
evidence_type: EXP
original_reference_id: PMID:38297129
qualifier: enables
review:
summary: >-
Experimental (EXP) annotation of Delta(7)-sterol 5(6)-desaturase activity
from the Nature ferroptosis study, which characterized SC5D FUNCTION and
CATALYTIC ACTIVITY as the enzyme producing 7-DHC. Confirms the core
catalytic function.
action: ACCEPT
reason: >-
Experimental support for the precise reaction; underpins the UniProt
CATALYTIC ACTIVITY entries. Core molecular function.
supported_by:
- reference_id: PMID:38297129
supporting_text: "an unexpected prosurvival"
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Catalyzes the penultimate step"
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: IDA
original_reference_id: PMID:10786622
qualifier: is_active_in
review:
summary: >-
Experimental (IDA) determination that SC5D is an integral endoplasmic
reticulum membrane protein, from the cloning study that also demonstrated
the enzymatic activity by yeast-mutant complementation.
action: ACCEPT
reason: >-
Primary experimental evidence for the ER-membrane location; the core
cellular component for this enzyme.
supported_by:
- reference_id: PMID:10786622
supporting_text: "Mammalian SC5D was presumed as an integral"
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Endoplasmic reticulum membrane"
- term:
id: GO:0006695
label: cholesterol biosynthetic process
evidence_type: IDA
original_reference_id: PMID:10786622
qualifier: involved_in
review:
summary: >-
Experimental (IDA) annotation to cholesterol biosynthetic process from the
cloning/complementation study, which functionally showed SC5D introduces
the C5-6 double bond into lathosterol in cholesterol biosynthesis. This is
the correct core biological process.
action: ACCEPT
reason: >-
Direct experimental support for SC5D's role in cholesterol biosynthesis.
A more specific child term (GO:0033490, cholesterol biosynthetic process
via lathosterol) is proposed separately as a NEW annotation to capture the
precise lathosterol arm.
supported_by:
- reference_id: PMID:10786622
supporting_text: "introduce C5-6 double bond into lathosterol in cholesterol biosynthesis"
- term:
id: GO:0033490
label: cholesterol biosynthetic process via lathosterol
evidence_type: IDA
original_reference_id: PMID:10786622
qualifier: involved_in
review:
summary: >-
Proposed more specific annotation: SC5D acts in the lathosterol arm of
cholesterol biosynthesis, catalyzing lathosterol -> 7-dehydrocholesterol.
UniProt assigns this precise child term (GO:0033490, IDA:UniProtKB); it is
not yet in GOA and is added here as a NEW, more informative annotation.
action: NEW
reason: >-
Sharper than the generic GO:0006695: the lathosterol-specific arm is the
exact pathway context of the SC5D reaction, matching the UniProt IDA
annotation.
supported_by:
- reference_id: PMID:10786622
supporting_text: "introduce C5-6 double bond into lathosterol in cholesterol biosynthesis"
- term:
id: GO:0050046
label: delta7-sterol 5(6)-desaturase activity
evidence_type: IDA
original_reference_id: PMID:10786622
qualifier: enables
review:
summary: >-
Experimental (IDA) annotation of Delta(7)-sterol 5(6)-desaturase activity.
The human cDNA functionally complemented a sterol-C5-desaturase-defective
yeast mutant, directly demonstrating the catalytic activity.
action: ACCEPT
reason: >-
Direct experimental demonstration of the core catalytic function via
yeast complementation.
supported_by:
- reference_id: PMID:10786622
supporting_text: "functional complementation of a defective yeast mutant proves that the human and"
- term:
id: GO:0110076
label: negative regulation of ferroptosis
evidence_type: IMP
original_reference_id: PMID:38297129
qualifier: involved_in
review:
summary: >-
Loss-of-function (IMP) evidence that SC5D negatively regulates ferroptosis.
As a distal-cholesterol-biosynthesis enzyme, SC5D produces 7-DHC, a potent
radical-trapping sterol that shields (phospho)lipids from autoxidation;
loss of SC5D lowers 7-DHC and sensitizes cells to ferroptosis. This is a
real but indirect, non-core role mediated by the 7-DHC product.
action: KEEP_AS_NON_CORE
reason: >-
Supported experimentally, but the effect is a downstream/indirect
consequence of SC5D's catalytic product (7-DHC) rather than a distinct
molecular activity of SC5D itself; the core function is C5-sterol
desaturation in cholesterol biosynthesis. Keep as a non-core process.
supported_by:
- reference_id: PMID:38297129
supporting_text: "we now show that 7-DHC accumulation"
- term:
id: GO:0110076
label: negative regulation of ferroptosis
evidence_type: IMP
original_reference_id: PMID:38297130
qualifier: involved_in
review:
summary: >-
Loss-of-function (IMP) evidence from a genome-wide CRISPR screen: SC5D is
an anti-ferroptotic distal-cholesterol-biosynthesis gene. SC5D knockout
increased ferroptosis susceptibility and lowered 7-DHC, and re-expression
rescued the phenotype. Indirect, non-core role via the 7-DHC product.
action: KEEP_AS_NON_CORE
reason: >-
Well supported experimentally in this full-text study, but mechanistically
the protection is conferred by the SC5D reaction product 7-DHC, not by an
independent SC5D activity; keep as a non-core biological process.
supported_by:
- reference_id: PMID:38297130
supporting_text: "individual deletion of CYP51A1, MSMO1, EBP and SC5D in HEK293T cells increased the susceptibility to ferroptosis"
- reference_id: PMID:38297130
supporting_text: "Re-expression of SC5D reversed the severity of ferroptosis induced by RSL3 in SC5D KO cells"
- term:
id: GO:0000248
label: C-5 sterol desaturase activity
evidence_type: EXP
original_reference_id: PMID:12189593
qualifier: enables
review:
summary: >-
Experimental (EXP) annotation of C-5 sterol desaturase activity based on
the first human lathosterolosis patient, in whom the SC5D-catalyzed
conversion of lathosterol to 7-dehydrocholesterol was blocked and the
enzyme activity was deficient. Supports the core catalytic function.
action: ACCEPT
reason: >-
Human patient data directly link SC5D to C-5 sterol desaturase activity
(loss of activity blocks lathosterol -> 7-DHC). Core molecular function.
supported_by:
- reference_id: PMID:12189593
supporting_text: "showing a block in the conversion of lathosterol into"
- reference_id: PMID:12189593
supporting_text: "was deficient in the patient's"
- term:
id: GO:0000248
label: C-5 sterol desaturase activity
evidence_type: EXP
original_reference_id: PMID:12812989
qualifier: enables
review:
summary: >-
Experimental (EXP) annotation of C-5 sterol desaturase activity supported
by the human patient and Sc5d-null mouse study, which established that
lathosterol 5-desaturase catalyzes the conversion of lathosterol to
7-dehydrocholesterol in the next-to-last step of cholesterol synthesis.
action: ACCEPT
reason: >-
Combined human and mouse loss-of-function evidence for the core catalytic
function; elevated lathosterol and decreased cholesterol on enzyme loss.
supported_by:
- reference_id: PMID:12812989
supporting_text: "catalyzes the conversion of lathosterol to"
- reference_id: PMID:12812989
supporting_text: "had elevated lathosterol and decreased cholesterol"
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-1655852
qualifier: located_in
review:
summary: >-
Reactome (TAS) ER-membrane localization associated with expression of
lathosterol oxidase (SC5D). Consistent with the experimental IDA and the
multi-pass membrane topology.
action: ACCEPT
reason: >-
Redundant with the experimentally determined ER membrane location; correct
core cellular component.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Endoplasmic reticulum membrane"
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-195664
qualifier: located_in
review:
summary: >-
Reactome (TAS) ER-membrane localization for the SC5D-catalyzed desaturation
of cholesta-7,24-dien-3beta-ol (a Bloch-arm reaction). Consistent with the
established ER location.
action: ACCEPT
reason: >-
Correct core cellular component; the reaction it is attached to takes place
in the ER, as noted by Reactome, and matches the human IDA.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Endoplasmic reticulum membrane"
- term:
id: GO:0005789
label: endoplasmic reticulum membrane
evidence_type: TAS
original_reference_id: Reactome:R-HSA-6807053
qualifier: located_in
review:
summary: >-
Reactome (TAS) ER-membrane localization for the SC5D reaction that
desaturates lathosterol to 7-dehydrocholesterol. Consistent with the
experimental and predicted ER-membrane location.
action: ACCEPT
reason: >-
Correct core cellular component; matches human IDA and topology.
supported_by:
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Endoplasmic reticulum membrane"
core_functions:
- description: >-
Lathosterol oxidase / Delta(7)-sterol C5(6)-desaturase that introduces the
C5-6 double bond into lathosterol to form 7-dehydrocholesterol, the
penultimate step of cholesterol biosynthesis, acting in the endoplasmic
reticulum membrane.
molecular_function:
id: GO:0050046
label: delta7-sterol 5(6)-desaturase activity
directly_involved_in:
- id: GO:0006695
label: cholesterol biosynthetic process
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
supported_by:
- reference_id: PMID:10786622
supporting_text: "introduce C5-6 double bond into lathosterol in cholesterol biosynthesis"
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Catalyzes the penultimate step"
- description: >-
C-5 sterol desaturase activity: family-level oxidoreductase function that
installs the Delta(5) double bond of sterols, dependent on a non-heme di-iron
center coordinated by conserved histidine-box motifs, driving the lathosterol
arm of cholesterol biosynthesis.
molecular_function:
id: GO:0000248
label: C-5 sterol desaturase activity
directly_involved_in:
- id: GO:0033490
label: cholesterol biosynthetic process via lathosterol
locations:
- id: GO:0005789
label: endoplasmic reticulum membrane
supported_by:
- reference_id: PMID:12812989
supporting_text: "catalyzes the conversion of lathosterol to"
- reference_id: file:human/SC5D/SC5D-uniprot.txt
supporting_text: "Belongs to the sterol desaturase family"
proposed_new_terms: []
suggested_questions:
- question: >-
Is SC5D's role in modulating ferroptosis (via 7-DHC) physiologically
relevant in normal tissues, or primarily a cancer-context phenomenon?
- question: >-
To what extent does SC5D contribute to the Bloch versus Kandutsch-Russell
arms of cholesterol biosynthesis in different human tissues?
suggested_experiments:
- description: >-
Reconstitute purified human SC5D with cytochrome b5 / cytochrome b5 reductase
to measure the di-iron-dependent desaturation kinetics on lathosterol versus
5alpha-cholesta-7,24-dien-3beta-ol and confirm cofactor stoichiometry.
hypothesis: >-
SC5D is a non-heme di-iron desaturase that uses electrons from cytochrome b5
to desaturate multiple Delta(7)-sterol substrates.
- description: >-
Site-directed mutagenesis of the three histidine-box motifs to test their
requirement for iron binding and catalysis, complementing the disease-variant
(R29Q, Y46S, G211D) structure-function analysis.
hypothesis: >-
The conserved histidine-box motifs coordinate the catalytic di-iron center
and are essential for C5-sterol desaturase activity.
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000107
title: Automatic transfer of experimentally verified manual GO annotation data to
orthologs using Ensembl Compara
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: file:human/SC5D/SC5D-uniprot.txt
title: UniProtKB entry O75845 (SC5D_HUMAN), Lathosterol oxidase
findings: []
- id: PMID:10786622
title: cDNA cloning of the mammalian sterol C5-desaturase and the expression in
yeast mutant.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Cloning and yeast-complementation study establishing SC5D catalytic
activity and ER-membrane localization; source of the UniProt RecName, EC
number, and subcellular location. Abstract-only in cache but claims
confirmed against the UniProt record.
- id: PMID:12189593
title: Lathosterolosis, a novel multiple-malformation/mental retardation syndrome
due to deficiency of 3beta-hydroxysteroid-delta5-desaturase.
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
First human lathosterolosis patient (R29Q, G211D); documents block in
lathosterol to 7-DHC conversion and deficient SC5D activity.
- id: PMID:12812989
title: 'Lathosterolosis: an inborn error of human and murine cholesterol synthesis
due to lathosterol 5-desaturase deficiency.'
findings: []
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Sc5d-null mouse and human Y46S patient; states SC5D catalyzes the
next-to-last step of cholesterol synthesis; elevated lathosterol / reduced
cholesterol on loss.
- id: PMID:38297129
title: 7-Dehydrocholesterol is an endogenous suppressor of ferroptosis.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Nature study characterizing SC5D function/catalytic activity/pathway and
the anti-ferroptotic role of its product 7-DHC. Abstract-only in cache; the
ferroptosis role is indirect (via 7-DHC), hence treated as non-core.
- id: PMID:38297130
title: 7-Dehydrocholesterol dictates ferroptosis sensitivity.
findings: []
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Full text available; genome-wide CRISPR screen shows SC5D is an
anti-ferroptotic distal-cholesterol-biosynthesis gene whose product 7-DHC
suppresses ferroptosis. Supports GO:0110076 as a non-core role.
- id: Reactome:R-HSA-1655852
title: Expression of Lathosterol Oxidase (SC5D, SC5DL)
findings: []
- id: Reactome:R-HSA-195664
title: Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol
findings: []
- id: Reactome:R-HSA-6807047
title: Cholesterol biosynthesis via desmosterol (Bloch pathway)
findings: []
- id: Reactome:R-HSA-6807053
title: SC5D desaturates LTHSOL to 7-dehydroCHOL
findings: []
- id: Reactome:R-HSA-9969901
title: Cholesterol biosynthesis from zymosterol (modified Kandutsch-Russell pathway)
findings: []