PAINT: human genes with no IBA

Reviewing the genes that phylogenetic annotation does not reach

AI Gene Review · projects/PAINT · 2026

Bottom line

  • 7,593 human genes (7,524 symbols) had no IBA annotation; each gets 2 deep-research reports and a full review of its GO rows.
  • 715 reviews complete, 24,409 decisions: 11,926 accepted, 2,778 over-annotated, 1,338 removed, 902 NEW proposals.
  • Lessons: the no-IBA list is stale; the real gap is families with no MF IBD; names mislead (PLD3/PLD4 are exonucleases).

Why these genes

  • A PAINT curator places a function at a tree node (IBD); descendants inherit it as IBA.
  • A human gene with no IBA may be poorly characterized, divergent, or lack orthologs with experimental evidence.
  • These are the genes where literature review adds most, and where a missing or misplaced node shows up.

Where IBAs come from, and where they fail

Per-gene workflow

just fetch-gene human GENE
just deep-research human GENE --provider falcon
just deep-research human GENE --provider cyberian
# review every row in GENE-ai-review.yaml
just validate human GENE
  • The 2026-09-04 batch added a paired PANTHER FamilyReview for each gene's family (19 written).

Results

Example: a misleading name

PLD3 review page. PLD3 and PLD4 are 5'-3' exonucleases despite the name "phospholipase D"; PLD5 is catalytically inactive.

Findings from the 2026-09-04 batch

  1. Stale source list: PEX11B, ORMDL3, CFAP61, LOXHD1, BCKDHA/B, PEX13, PEX16, MTCH2, MBL2 now receive IBAs.
  2. Real gap: no molecular-function IBD for BCKDH E1, PEX13, PEX16, NDUFV1's eukaryotic node.
  3. PTHR48178 (PEX2): Cdc73/Paf1 complex IBD from a PAF1 homonym → WRONG_NODE.
  4. NAALADL2 descends from the carboxypeptidase IBD node yet gets no IBA; an explicit IRD recommended, with a residue check showing loss of the catalytic Glu pair.

Status and next steps

  • 715 of 7,524 listed genes complete (about 9.5%); the page's status table (635, 2026-09-04) predates this count.
  • Open: re-derive the no-IBA list against current GOA; re-fetch IL10 GOA; scale deep research.

Read more: projects/PAINT.md · projects/paint/human-no-IBA-simple.csv · interpro/panther/<PTHR>/