C. elegans ciliopathy genes

Reviewing GO annotations for 20 genes that build and run worm sensory cilia

AI Gene Review · projects/CAEEL_CILIOPATHY · 2026

Bottom line

  • Worm sensory cilia use the same machinery that fails in human ciliopathies: DAF-19, IFT motors and trains, the BBSome, the MKS/NPHP transition zone, LOV-1/PKD-2.
  • We reviewed every GO annotation on 20 genes: 482 rows, 366 ACCEPT, 29 MODIFY, 8 REMOVE, 21 NEW proposals.
  • Most annotations are sound. Errors cluster in over-general terms and propagation from vertebrate motile-cilium and Hedgehog biology.

Why the worm

  • 60 of 302 neurons are ciliated; cilia are non-motile, like vertebrate primary cilia.
  • Classic screens (Dyf, Osm, Che, Daf, Lov phenotypes) named much of the IFT machinery.
  • Worm GO annotations feed orthology-based inference for human BBS, NPHP, MKS and PKD genes.
  • Test: does per-gene review separate real worm biology from propagated vertebrate biology?

Where the 20 genes act

What a review looks like

bbs-1 review page: BBSome membership (GO:0034464) accepted; the IBA centrosome row modified to ciliary basal body.

Actions per gene

Typical corrections

Gene Existing term Action Replacement
osm-3 microtubule-based movement (IEA) MODIFY intraciliary anterograde transport
che-3 intracellular protein localization (IMP) MODIFY intraciliary retrograde transport
nphp-1 ciliary basal body (IDA) MODIFY ciliary transition zone
mksr-2 cilium (IEA) MODIFY ciliary transition zone
bbs-2 motile cilium (IBA) MODIFY non-motile cilium
pef-1 nucleus (IBA), iron ion binding (IEA) REMOVE none

All rows verified in genes/worm/<gene>/<gene>-ai-review.yaml.

Findings

  1. Species-inappropriate propagation: motile-cilium rows on dynein CHE-3 and patched/smoothened binding on BBS-1 removed.
  2. Precision: generic transport and localization terms sharpened to anterograde/retrograde IFT, basal body, transition zone.
  3. Missing functions proposed: transition zone assembly for mks-1 and mks-3; axoneme and thermosensory behaviour for pef-1.
  4. pkd-2 (60 rows) and mks-6 (11 rows): every row accepted.

Status and next steps

  • ✅ 20/20 gene reviews, pathway summary, curation recommendations.
  • ⬜ Submit the MODIFY/REMOVE/NEW recommendations to WormBase/GO.
  • ⬜ Fold in 8 IFT genes already reviewed outside this project (daf-10, che-11, dyf-2, che-13, xbx-1, dyf-1, osm-6, klp-11).

Read more: projects/CAEEL_CILIOPATHY.md · projects/CAEEL_CILIOPATHY/ · genes/worm/<gene>/