STBD1

Summary: Bare membrane propagated phylogenetically; uninformative for a protein whose specific membrane anchor is known.

Reason: Same shape as the SL project's pattern A (bare parent retained alongside a specific child), reached here by phylogenetic propagation. STBD1 carries GO:0005789 endoplasmic reticulum membrane with experimental support and is a single-pass type III membrane protein, so the bare parent adds nothing. The objection is to granularity only; the IBA itself is sound, and the WITH/FROM column listing UniProtKB:O95210 alongside the PANTHER node reflects that this gene's own experimental annotation helped the curator place the ancestral assertion. See projects/SL.md for the pattern.

Summary: Lysosomal transport; glycogen delivery to lysosomes is the outcome of glycophagy.

Reason: Supported by the colocalization of STBD1 with glycogen and LAMP1 and by the trafficking of glycogen to lysosomes.

Summary: Cargo receptor for glycogen; the gene's core molecular function, but stated at the generic cargo-receptor level rather than the autophagy-specific one.

Reason: STBD1 binds glycogen through its CBM20 domain and an ATG8-family protein through its AIM/LIR, physically bridging cargo to the autophagic machinery. This receptor role is what the gene is for, and GO:0160247 autophagy cargo adaptor activity states it exactly: "the binding activity of a molecule that brings together a cargo, targeted for degradation via autophagy, to a phagophore", carrying "selective autophagy receptor activity" as a synonym. The generic GO:0038024 parent drops the autophagic context that is the whole point of the function, and this corpus already uses GO:0160247 for every other selective-autophagy receptor it has reviewed (TAX1BP1, NBR1, NCOA4, CALCOCO2, CCDC50). Both source annotations here are electronic or phylogenetic (IBA from GO_REF:0000033, IEA from GO_REF:0000107), so no experimental curation is being overruled.

Proposed replacements: autophagy cargo adaptor activity

Summary: Glycophagy, the selective autophagy route STBD1 defines.

Reason: Core process. STBD1 is the receptor that makes glycogen an autophagic substrate, so this is not merely participation in a route but constitutive of it.

Summary: Endoplasmic reticulum membrane; STBD1 is a single-pass type III membrane protein anchored there.

Reason: Experimentally supported. The N-terminal hydrophobic segment is the membrane anchor - deleting it gives a diffuse cytoplasmic distribution.

Summary: Vesicle-mediated transport, a broad parent of the specific trafficking terms.

Reason: Uninformative relative to GO:0007041 and GO:0061753, both present with better support.

Summary: Carbohydrate binding, the uninformative parent of glycogen binding.

Reason: True but less informative than GO:2001069, which carries the specific evidence.

Summary: T-tubule; a muscle-specific location for a protein most studied in liver and muscle glycogen metabolism.

Reason: Directly observed in muscle, near junctional sarcoplasmic reticulum. Real but tissue-restricted, so peripheral to the general cargo-receptor function.

Summary: Phagophore assembly site membrane; the cited evidence shows perinuclear and lysosomal colocalization, not a PAS membrane.

Reason: This is the STBD1 row of the section 5.4 triage in GO issue #29437, listed there under 'no evident support - review for removal'. Reading the primary paper confirms that reading. PMID:20810658 places Stbd1 at enlarged perinuclear structures colocalized with glycogen, the late endosomal/lysosomal marker LAMP1, and GABARAPL1; it never examines the phagophore assembly site. Colocalization with an ATG8-family protein has been over-read into residence in a PAS membrane. GO:0034045 additionally asserts via bounding_layer_of a bounding membrane that the PAS, a protein condensate, does not have (PMID:32025038). No replacement term is proposed because the supported locations - GO:0048471 perinuclear region and the ER membrane - are already annotated on this gene, so there is nothing to move.

Summary: Glycogen binding via the C-terminal CBM20 carbohydrate-binding module.

Reason: Direct and specific; the cargo half of the receptor function. CBM20 point mutations leave STBD1 perinuclear but abolish glycogen concentration there, separating binding from targeting.

Summary: Starch binding, a CBM20 domain-derived inference with no mammalian substrate.

Reason: The CBM20 module is named for starch binding in microbial and plant enzymes, and the term transfers with the domain. Mammals do not make starch; the physiological ligand is glycogen, already annotated as GO:2001069. This is a domain-family inference that does not survive organism context.

Summary: Bare protein binding from nine IPI experiments.

Reason: Per project curation guidance, protein binding does not describe what the gene product does. The underlying interactions with GABARAP/GABARAPL1 are the mechanistic basis of the accepted cargo receptor activity and are better expressed there.

Summary: Bare protein binding from nine IPI experiments.

Reason: Per project curation guidance, protein binding does not describe what the gene product does. The underlying interactions with GABARAP/GABARAPL1 are the mechanistic basis of the accepted cargo receptor activity and are better expressed there.

Summary: Bare protein binding from nine IPI experiments.

Reason: Per project curation guidance, protein binding does not describe what the gene product does. The underlying interactions with GABARAP/GABARAPL1 are the mechanistic basis of the accepted cargo receptor activity and are better expressed there.

Summary: Bare protein binding from nine IPI experiments.

Reason: Per project curation guidance, protein binding does not describe what the gene product does. The underlying interactions with GABARAP/GABARAPL1 are the mechanistic basis of the accepted cargo receptor activity and are better expressed there.

Summary: Bare protein binding from nine IPI experiments.

Reason: Per project curation guidance, protein binding does not describe what the gene product does. The underlying interactions with GABARAP/GABARAPL1 are the mechanistic basis of the accepted cargo receptor activity and are better expressed there.

Summary: Bare protein binding from nine IPI experiments.

Reason: Per project curation guidance, protein binding does not describe what the gene product does. The underlying interactions with GABARAP/GABARAPL1 are the mechanistic basis of the accepted cargo receptor activity and are better expressed there.

Summary: Lysosomal transport; glycogen delivery to lysosomes is the outcome of glycophagy.

Reason: Supported by the colocalization of STBD1 with glycogen and LAMP1 and by the trafficking of glycogen to lysosomes.

Summary: Cargo receptor for glycogen; the gene's core molecular function, but stated at the generic cargo-receptor level rather than the autophagy-specific one.

Reason: STBD1 binds glycogen through its CBM20 domain and an ATG8-family protein through its AIM/LIR, physically bridging cargo to the autophagic machinery. This receptor role is what the gene is for, and GO:0160247 autophagy cargo adaptor activity states it exactly: "the binding activity of a molecule that brings together a cargo, targeted for degradation via autophagy, to a phagophore", carrying "selective autophagy receptor activity" as a synonym. The generic GO:0038024 parent drops the autophagic context that is the whole point of the function, and this corpus already uses GO:0160247 for every other selective-autophagy receptor it has reviewed (TAX1BP1, NBR1, NCOA4, CALCOCO2, CCDC50). Both source annotations here are electronic or phylogenetic (IBA from GO_REF:0000033, IEA from GO_REF:0000107), so no experimental curation is being overruled.

Proposed replacements: autophagy cargo adaptor activity

Summary: Glycophagy, the selective autophagy route STBD1 defines.

Reason: Core process. STBD1 is the receptor that makes glycogen an autophagic substrate, so this is not merely participation in a route but constitutive of it.

Summary: Substrate localization to autophagosome; the mechanistic statement of the receptor role.

Reason: Describes what the cargo receptor actually accomplishes, and is more informative than the generic transport terms.

Summary: Endoplasmic reticulum membrane; STBD1 is a single-pass type III membrane protein anchored there.

Reason: Experimentally supported. The N-terminal hydrophobic segment is the membrane anchor - deleting it gives a diffuse cytoplasmic distribution.

Summary: Phagophore assembly site membrane; the cited evidence shows perinuclear and lysosomal colocalization, not a PAS membrane.

Reason: This is the STBD1 row of the section 5.4 triage in GO issue #29437, listed there under 'no evident support - review for removal'. Reading the primary paper confirms that reading. PMID:20810658 places Stbd1 at enlarged perinuclear structures colocalized with glycogen, the late endosomal/lysosomal marker LAMP1, and GABARAPL1; it never examines the phagophore assembly site. Colocalization with an ATG8-family protein has been over-read into residence in a PAS membrane. GO:0034045 additionally asserts via bounding_layer_of a bounding membrane that the PAS, a protein condensate, does not have (PMID:32025038). No replacement term is proposed because the supported locations - GO:0048471 perinuclear region and the ER membrane - are already annotated on this gene, so there is nothing to move.

Summary: Lysosomal transport; glycogen delivery to lysosomes is the outcome of glycophagy.

Reason: Supported by the colocalization of STBD1 with glycogen and LAMP1 and by the trafficking of glycogen to lysosomes.

Summary: Polysaccharide binding, another parent of glycogen binding.

Reason: Same reasoning as carbohydrate binding; retained as a high-level default.

Summary: Bare protein binding from nine IPI experiments.

Reason: Per project curation guidance, protein binding does not describe what the gene product does. The underlying interactions with GABARAP/GABARAPL1 are the mechanistic basis of the accepted cargo receptor activity and are better expressed there.

Summary: Bare protein binding from nine IPI experiments.

Reason: Per project curation guidance, protein binding does not describe what the gene product does. The underlying interactions with GABARAP/GABARAPL1 are the mechanistic basis of the accepted cargo receptor activity and are better expressed there.

Summary: Endoplasmic reticulum, parent of the membrane term already supported.

Reason: Less informative than GO:0005789 for a single-pass membrane protein.

Summary: Endoplasmic reticulum, parent of the membrane term already supported.

Reason: Less informative than GO:0005789 for a single-pass membrane protein.

Summary: Plasma membrane; the parent under which the sarcolemma/T-tubule observation sits.

Reason: Retained as context for the muscle localization rather than as a general residence.

Summary: Enzyme binding, an uninformative binding term.

Reason: Names no partner and no function. STBD1's meaningful interactions - GABARAP and GABARAPL1 via its AIM/LIR, and glycogen-associated enzymes such as GYS2 - are better captured by the cargo receptor and glycogen binding terms already accepted.

Summary: T-tubule; a muscle-specific location for a protein most studied in liver and muscle glycogen metabolism.

Reason: Directly observed in muscle, near junctional sarcoplasmic reticulum. Real but tissue-restricted, so peripheral to the general cargo-receptor function.

Summary: Perinuclear region of cytoplasm, the location directly observed for STBD1 and its glycogen cargo.

Reason: Directly observed. Overexpressed Stbd1 concentrates at enlarged perinuclear structures colocalized with glycogen, LAMP1 and GABARAPL1, and the localization survives CBM20 point mutation while glycogen concentration does not.

Summary: Plasma membrane; the parent under which the sarcolemma/T-tubule observation sits.

Reason: Retained as context for the muscle localization rather than as a general residence.

Summary: Plasma membrane; the parent under which the sarcolemma/T-tubule observation sits.

Reason: Retained as context for the muscle localization rather than as a general residence.

Summary: Tertiary granule membrane, from neutrophil organelle proteomics.

Reason: High-throughput compartment proteomics in one cell type. Not false, but it reflects where the protein was detected in a specific granulocyte fractionation rather than a functional location.

Summary: Ficolin-1-rich granule membrane, from the same neutrophil proteomics series.

Reason: Same basis and same caveat as the tertiary granule membrane annotation.

Summary: Bare protein binding from nine IPI experiments.

Reason: Per project curation guidance, protein binding does not describe what the gene product does. The underlying interactions with GABARAP/GABARAPL1 are the mechanistic basis of the accepted cargo receptor activity and are better expressed there.

Summary: Glycogen catabolic process; STBD1 delivers glycogen for degradation but does not catabolize it.

Reason: STBD1 has no glycosidase activity. It participates by supplying substrate to the lysosomal route, so the term is defensible as pathway membership but is not a statement of this gene product's activity. Kept as non-core rather than removed.

Summary: Bare membrane from the same experiment that established the specific ER-membrane localization; the parent is redundant with its own child.

Reason: PMID:20810658 is the paper that showed STBD1 is anchored by its N-terminal hydrophobic segment and localizes to the ER and perinuclear membranes, and it also underlies the GO:0005789 annotation on this gene. Recording the bare parent alongside the child from the same experiment adds no information. Not false, only empty. Same shape as the SL project's pattern A, though the evidence here is direct rather than GO_REF:0000044.

Summary: Perinuclear region of cytoplasm, the location directly observed for STBD1 and its glycogen cargo.

Reason: Directly observed. Overexpressed Stbd1 concentrates at enlarged perinuclear structures colocalized with glycogen, LAMP1 and GABARAPL1, and the localization survives CBM20 point mutation while glycogen concentration does not.

Summary: Glycophagy, the selective autophagy route STBD1 defines.

Reason: Core process. STBD1 is the receptor that makes glycogen an autophagic substrate, so this is not merely participation in a route but constitutive of it.

Summary: Glycogen binding via the C-terminal CBM20 carbohydrate-binding module.

Reason: Direct and specific; the cargo half of the receptor function. CBM20 point mutations leave STBD1 perinuclear but abolish glycogen concentration there, separating binding from targeting.