pomt2 notes

2026-05-09 review notes

Reviewed GOA, UniProt F1Q8R9, PMID:20466645, PMID:36499139, and PANTHER family cache. The core annotation is the ER protein O-mannosyltransferase role; photoreceptor maintenance is retained as a non-core downstream phenotype/process consequence of O-mannosyl glycan loss.

Re-review 2026-09-29

Re-reviewed all 12 GOA rows against the two cached primary papers and UniProt F1Q8R9 (the yaml
review blocks had been rewritten in an earlier interrupted pass; this pass verified them,
confirmed zero validation errors, and completed the notes/history records).

• Core activity GO:0004169 (IBA, IEA/EC, IGI): ACCEPT. The zebrafish enzyme was reconstituted
  directly PMID:20466645, and
  UniProt derives EC 2.4.1.109 from that paper. The zebrafish gene appearing in its own IBA
  WITH/FROM is expected (its IGI seeded the PAINT node), not circular.
• Core process GO:0035269 (IBA, IGI): ACCEPT; participation is direct (Pomt2 catalyses the
  initiating mannose transfer) [PMID:20466645 "the IIH6 reactivity was lost in both zPOMT1 and
  zPOMT2 morphants"; PMID:36499139 "pomt2 mutation resulted in a loss of matriglycan"].
• Generic parents GO:0000030 mannosyltransferase activity, GO:0006493 protein O-linked
  glycosylation and GO:0016020 membrane (InterPro/ARBA IEA): MODIFY to the specific child
  terms already carried (GO:0004169, GO:0035269, GO:0005789).
• Localization GO:0005783 (IBA) / GO:0005789 (ISS, IEA SubCell): ACCEPT, supported by the
  SUBCELLULAR LOCATION line and the 11-TM topology, not by the FUNCTION line.
• GO:0045494 photoreceptor cell maintenance (IMP, PMID:36499139, full text cached):
  KEEP_AS_NON_CORE. The protective effect is executed downstream by matriglycan-dependent EYS
  anchoring PMID:36499139; Pomt2 itself does no work in photoreceptor
  maintenance. GOA already uses acts_upstream_of_or_within.
• PMID:20466645 is abstract-only in the cache; all quotes are from the abstract.
• Validation: zero errors; one residual warning (no deep-research citation), left as is because
  primary literature covers every claim.

Follow-up after PR review (2026-10-09)

• Decided to keep core_functions[0].molecular_function: GO:0004169 (not contributes_to_molecular_function). Distinction from dph2 stated in the core description and the IGI row reason: Pomt2 is itself a GT39-fold catalytic subunit (both subunits of the obligate Pomt1-Pomt2 heteromer carry the glycosyltransferase fold), whereas dph2 is a non-catalytic electron-donor subunit. GOA qualifier on all three zebrafish GO:0004169 rows is enables, and QuickGO shows human POMT2 (Q9UKY4) also annotated enables GO:0004169 (IBA GO_REF:0000033 and IEA GO_REF:0000003), so curators do not use contributes_to for this subunit.
• Added in_complex: GO:0031502 dolichyl-phosphate-mannose-protein mannosyltransferase complex (verified in QuickGO; human POMT1/POMT2 are part_of it by IPI on PMID:16698797). Validation: zero errors; a new warning notes GO:0031502 is not in existing_annotations (no NEW row added, per the batch instruction to report rather than add), plus the pre-existing deep-research warning.