gnptab (Danio rerio) review notes

Batch 05 curation notes

• Core interpretation: gnptab encodes the alpha/beta precursor of UDP-N-acetylglucosamine:lysosomal-enzyme N-acetylglucosamine-1-phosphotransferase, a Golgi enzyme that initiates mannose-6-phosphate tagging of lysosomal hydrolases. The core function is GlcNAc-1-phosphotransferase activity in N-glycan processing to lysosome; craniofacial, cartilage, bone, and heart phenotypes are downstream consequences of impaired lysosomal enzyme targeting.
• Key UniProt support: Catalyzes the formation of mannose 6-phosphate (M6P) markers.
• Existing GOA annotations were reviewed against this core role; broad, inferred, or downstream phenotype annotations were kept as non-core unless they overstate the direct function.

Re-review 2026-09-29

• Rewrote every templated review block (31 rows, including 5 rows appended as PENDING from the refreshed GOA: duplicate IMP rows for chondrocyte development, heart morphogenesis and embryonic cranial skeleton morphogenesis from second ZFIN genotype/morpholino records, plus IBA rows for protein N-linked glycosylation and lysosome organization). Deep-research quotes were dropped as support; the primary zebrafish papers are cached and are now quoted.
• Core activity (GO:0003976, all 7 rows ACCEPT) is grounded on zebrafish data: PMID:19834066 and the mRNA rescue in PMID:23733939.
• Localization rows (Golgi apparatus, Golgi membrane) now cite the UniProt SUBCELLULAR LOCATION line ("Golgi apparatus membrane") and PMID:26404503 instead of the FUNCTION line.
• Action changes: GO:0016772 (IEA, InterPro) KEEP_AS_NON_CORE -> MODIFY to GO:0003976; GO:0015031 protein transport (IEA, ARBA) KEEP_AS_NON_CORE -> MODIFY to GO:0016256 (GO:0015031 is an ancestor of GO:0016256 per QuickGO, so the generic term is redundant); GO:0005509 calcium ion binding (IEA) KEEP_AS_NON_CORE -> MARK_AS_OVER_ANNOTATED (EF-hand signature only, no calcium-binding evidence); GO:0046835 carbohydrate phosphorylation (ISS) KEEP_AS_NON_CORE -> ACCEPT (it is the chemistry of the enzyme's own reaction). New IBA GO:0006487 -> ACCEPT (ancestor of GO:0016256); new IBA GO:0007040 -> KEEP_AS_NON_CORE, consistent with the ISS row.
• Developmental IMP/IGI rows (heart morphogenesis, cartilage/bone development, viscerocranium and cranial skeleton morphogenesis, chondrocyte development) stay KEEP_AS_NON_CORE: the phenotypes are executed by mis-sorted cathepsin K [PMID:26404503 "Here we link extracellular cathepsin K activity to abnormal bone and cartilage development in MLII animals by demonstrating that it disrupts the balance of TGFß-related signaling during chondrogenesis."; PMID:33055423 "Importantly, cathepsin K inhibition restored normal heart and valve development in MLII embryos."]. The IGI partner ZFIN:ZDB-GENE-001205-4 resolves to ctsk.
• Added reference_review (all five PMIDs VERIFIED against cached titles; PMID:19834066 and PMID:25505245 are abstract-only caches), findings, a standalone description, two suggested questions and one experiment. Validation: 0 errors, 0 warnings.