gene_symbol	category	local_aigr_status	pn_annotations	why_interesting	suggested_next_step	related_project
BTF3	positive_control	local_review_complete_not_phase1	Translation > Cytosolic translation > Nascent peptide husbandry > Nascent peptide sorting > NAC component	True human BTF3 (P20290) is a reviewed PN translation factor; BTN3A3 synonym confusion was the original tracking concern	Add to boundary/phase1 tracking and use as NAC-component positive control	RIBOSOME_QUALITY_CONTROL.md
HSPA12A	domain_exception	local_review_complete_not_phase1	Cytonuclear proteostasis > Chaperone > HSP70 system > HSP70	MS1 inclusion is based on HSP70 architecture, but review supports SorLA/SORL1-tail adaptor trafficking rather than canonical HSP70 folding activity	Record as HSP70 GO:0140662 gene exception and sync the domain-only caveat to PN	UNFOLDED_PROTEIN_BINDING.md
HSPA12B	domain_exception	local_review_complete_not_phase1	Cytonuclear proteostasis > Chaperone > HSP70 system > HSP70	MS1 inclusion is based on HSP70 architecture, but review supports endothelial and ERAD/STING context rather than canonical HSP70 folding activity	Record as HSP70 GO:0140662 gene exception and sync the domain-only caveat to PN	UNFOLDED_PROTEIN_BINDING.md
AARSD1	isoform_context_exception	local_review_complete_not_phase1	Cytonuclear proteostasis > HSP90 cochaperone; Translation > tRNA synthetase	Review supports canonical AlaX translational proofreading as core and treats HSP90 cochaperone evidence as likely readthrough/fusion-isoform context	Record HSP90-cochaperone exception and keep canonical proofreading as the GO bridge outcome	not_recorded
BAG6	multibranch_boundary_case	local_review_complete_not_phase1	ER proteostasis > GET pathway component; UPS > associated non-Ub enzyme chaperone; UPS > UBL domain > chaperones and related	Review supports specific GET, ERAD, and holdase roles but not broad parent protein-transport propagation	Add to boundary/phase1 tracking; keep broad protein-transport exception and positive GET/ERAD bridge outcomes	ER_PHAGY.md
TTC28	cc_tpr_exception	local_review_complete_not_phase1	Cytonuclear proteostasis > Chaperone > HSP70-HSP90 system integration > HSP70-HSP90 joint cochaperone > TPR domain containing	Review supports HSPA8-mediated CMA/microautophagy substrate biology and mitotic scaffold function, not HSP90 cochaperone propagation	Record HSP90-cochaperone exception and preserve CMA-substrate versus core-mitosis distinction	not_recorded
STAT1	context_specific_ALP	local_review_complete_not_phase1	ALP > Autophagy gene expression > Transcriptional repressor	Workbook has an explicit ULK1-promoter note, but this likely remains a contextual non-core role	Create boundary/phase1 dossier and decide whether a non-core ALP regulatory annotation is warranted	INTEGRATED_STRESS_RESPONSE.md
BIRC6	contextual_autophagy	local_review_complete_not_phase1	ALP > Autophagosome-lysosome docking > Lysosome-autophagosome SNARE complex regulator; UPS > E2-E3 chimera; UPS > with intrinsic E2 > BIR repeat	PN assigns a specific ALP role beyond the already-known UPS and autophagy-suppression context	Create boundary/phase1 dossier and audit whether docking/fusion belongs as a secondary function	ER_PHAGY.md
CRYAA	ontology_gap_bridge	local_review_complete_not_phase1	Cytonuclear proteostasis > Chaperone > small HSP system > small HSP	Positive control where PN placement and UPB holdase logic strongly converge	Create bridge dossier for small-HSP holdase/foldase ontology-gap analysis	UNFOLDED_PROTEIN_BINDING.md
CRYAB	ontology_gap_bridge	local_review_complete_not_phase1	Cytonuclear proteostasis > small HSP; Mitochondrial proteostasis > small HSP; Extracellular proteostasis > chaperone	Shows how PN adds multi-branch context around a reviewed holdase gene	Create bridge dossier for multi-branch proteostasis semantics and small-HSP ontology gaps	UNFOLDED_PROTEIN_BINDING.md
SSR1	positive_control	local_review_complete_not_phase1	ER proteostasis > Protein transport > TRAP complex component	Good example where PN context is compatible with existing ER targeting/translocation GO terms	Add to boundary/phase1 tracking as a mapping positive control	ER_PHAGY.md
SSR2	positive_control	local_review_complete_not_phase1	ER proteostasis > Protein transport > TRAP complex component	Good example where PN context is compatible with existing ER targeting/translocation GO terms	Add to boundary/phase1 tracking as a mapping positive control	ER_PHAGY.md