Ciliary Basal Body-Plasma Membrane Docking — Obsoletion & Replacement

IN_PROGRESS OBSOLETION

Ciliary Basal Body-Plasma Membrane Docking — Obsoletion & Replacement

Overview

A GO obsoletion proposal will retire two ciliogenesis BP terms and merge their
annotations into the existing assembly term for the ciliary transition zone:

Both will be replaced by GO:1905349 ciliary transition zone assembly (BP).

The rationale, captured in the upstream go-ontology discussion, is that the
"docking" term as written actually describes the multi-step process of
transition zone assembly — including basal body recruitment, ciliary vesicle
docking, and plasma membrane fusion — rather than a single docking event.
Annotations are well-covered by the existing transition zone assembly term, so
the redundant/over-broad child can be retired. GO:1905353 (transition fiber
assembly) is being retired alongside it because there are no experimental
annotations to defend its existence and its scope overlaps with the same
assembly process.

This project tracks the impact on AI Gene Review and queues affected genes for
review, since none of the directly annotated genes are currently in this
repository.

Upstream tickets

Obsoletion plan (per upstream)

Obsoleted term ID Replacement
ciliary basal body-plasma membrane docking GO:0097711 GO:1905349 ciliary transition zone assembly
ciliary transition fiber assembly GO:1905353 GO:1905349 ciliary transition zone assembly

Affected experimental annotations (from upstream spreadsheet)

GO:0097711 has 7 experimental annotations across 6 groups. GO:1905353 has no
experimental annotations on the spreadsheet (an additional reason for its
retirement).

Group Gene Species UniProt / Source ID Reference Evidence Status
FlyBase Cby D. melanogaster FBgn0067317 PMID:27646273 IGI Removed (hattrill, 2026-05-04)
FlyBase dila D. melanogaster FBgn0033447 PMID:27646273 IGI Removed (hattrill, 2026-05-04)
MGI Cep290 M. musculus MGI:2384917 PMID:27002738 IMP move to GO:1905349
Reactome RAB3IP H. sapiens UniProtKB:Q96QF0 Reactome:R-HSA-5620912 TAS Reactome fixed; appears in June 2026 release
UniProt Cep290 D. melanogaster FBgn0035168 PMID:30013109 IMP move to GO:1905349
Xenbase foxj1.L X. laevis XB-GENE-856300 PMID:24048590 NAS move to GO:1905349
ZFIN pam D. rerio ZDB-GENE-090313-384 PMID:29540787 IMP move to GO:1905349

No InterPro2GO, UniProt-Keywords, or UniRule mappings to either term were
listed in the upstream issue.

Impact on this repo

No genes directly annotated to GO:0097711 or GO:1905353 are currently reviewed
here. Searches under genes/ for CEP290, RAB3IP, foxj1, and pam returned no
matches.

This means no existing reviews need refresh for the obsoletion itself, but
the propagated (IBA / electronic) ancestry of GO:0097711 reaches a much wider
set of ciliopathy genes — the GO API returns ~30 species-level entries for
CEP290 alone (the dominant PANTHER family for this term) plus other
transition-zone components — so the obsoletion is timely for any future
ciliopathy-focused reviews. The repo already has substantial cilia coverage
through the CAEEL_CILIOPATHY project (worm mks-1/3/5/6,
mksr-2, nphp-1/4, daf-19) and human INTU and TMEM67, so adding the
basal-body-docking-affected genes would strengthen that coverage.

Scope

Candidate genes for initial review

Verify each with just fetch-gene <organism> <gene> before starting and
confirm UniProt accessions. None are currently in the repo.

Tier 1 — high-priority, multi-disease ciliopathy gene

  1. CEP290 (human, UniProt O15078) — centrosomal protein 290; most
    heavily annotated gene under GO:0097711 across species (mouse, fly, fish
    all have direct annotations and the human gene receives IBA propagation
    from PTHR18879). Causal in Joubert syndrome, Leber congenital amaurosis 10,
    Meckel syndrome, Senior-Løken syndrome, and Bardet-Biedl syndrome. Strong
    functional literature on its role in transition zone assembly and ciliary
    gating; an excellent anchor review for the obsoletion.

Tier 2 — supporting ciliogenesis genes with direct annotations

  1. RAB3IP / Rabin8 (human, UniProt Q96QF0) — Rab3-interacting protein,
    guanine nucleotide exchange factor for Rab8a; the Reactome direct-annotation
    target. Important for ciliary vesicle delivery to the basal body — the very
    process that the obsoleted term partially described.
  2. FOXJ1 (Xenopus / human, NCBITaxon:8355 for the upstream NAS annotation)
    — master transcriptional regulator of motile ciliogenesis; the foxj1.L
    annotation is from PMID:24048590. A FOXJ1 review would also feed downstream
    ciliopathy and laterality projects.

Tier 3 — direct annotations, lower repo priority

  1. PAM (zebrafish, ZDB-GENE-090313-384) — peptidylglycine alpha-amidating
    monooxygenase ortholog; ZFIN annotation from PMID:29540787 (IMP). Less
    well-aligned with the repo's mammalian-and-canonical-model focus.
  2. Drosophila CEP290 (FBgn0035168) — the fly ortholog has its own direct
    annotation from UniProt, but a single human CEP290 review would cover the
    biology more efficiently than separate fly/mouse reviews.

Proposed approach

  1. Wait for the obsoletion to land. The upstream ontology ticket #31882 is
    still open at the time of writing (most recent activity 2026-05-04). FlyBase
    has already removed the two fly annotations and Reactome has fixed the
    RAB3IP entry for the June 2026 release; the remaining four direct
    annotations are pending action by MGI, UniProt, Xenbase, and ZFIN.
  2. Once the obsoletion is applied, regenerate GOA for any candidate gene
    that gets reviewed; the merged term GO:1905349 should appear in place of
    GO:0097711 for the IBA-propagated entries.
  3. Begin with CEP290 (human) as the anchor review. Its annotation portfolio
    is large enough to exercise the cilia / ciliopathy curation pattern, and it
    has direct experimental support across multiple species that all converge
    on the transition zone biology.
  4. Follow with RAB3IP as the second review — the GEF-for-Rab8a function is
    distinct from CEP290's structural role and would diversify the project's
    coverage of ciliogenesis machinery.
  5. Defer FOXJ1, fly CEP290, and zebrafish pam unless the broader cilia
    project explicitly expands to cover them; for the obsoletion-tracking
    purpose, CEP290 + RAB3IP are sufficient.
  6. Cross-reference with the parallel vesicle docking / vesicle tethering
    obsoletions     (#6379
    and #6375) — the
    ciliary-vesicle-tethering biology that the obsoleted term partially captured
    may be better represented by a prospective "vesicle membrane tethering
    activity" molecular function term (tracked in
    geneontology/go-annotation#6381;
    no GO identifier assigned yet) once that is in production.

Priority

Medium-low. The biology is well-established and there is strong existing
ciliopathy coverage in this repo to leverage, but no current reviews are
blocked by the obsoletion. This is opportunistic — CEP290 in particular is a
major unreviewed ciliopathy gene whose obsoletion-affected annotation makes
this a natural moment to tackle it.

Status