CFAP47 notes

Deep research status

Automated deep research was attempted and failed, so no CFAP47-deep-research-*.md
file exists for this gene:

• just deep-research human CFAP47 --provider falcon failed with
  Exception: Failed to authenticate (Edison/Falcon JWT authentication error).
• just deep-research human CFAP47 --provider perplexity failed with
  Provider 'perplexity' not available. Available: falcon, asta, openscientist.

Notes below come from a manual PubMed search (CFAP47[Title/Abstract], 18 hits,
2021-2026) and the cached publications. Every cited PMID was cached with
just fetch-pmid / just fetch-gene-pmids.

Identity

• UniProt Q6ZTR5 (CFA47_HUMAN); X-linked (Xp21.1); very large (canonical isoform 5,
  3,187 aa); UniProt annotates a calponin-homology (CH) domain (1746-1869) and InterPro
  Ig-like folds; the mouse structure (PMID:40473901) resolves a chain of numbered ASH
  domains with the CH domain in the "CFAP47-ring". PANTHER PTHR45912. Highly expressed in testis and present in sperm.
• Disease: X-linked spermatogenic failure 3 (SPGFX3, MIM:301059).

Structure: core of the central-apparatus bridge

• PMID:40473901 (in situ cryo-ET of mouse sperm central apparatus,
  full text).
• Knockout: PMID:40473901

Human genetics

• MMAF: PMID:33472045; an Australian man with a whole-gene Xp21.1 deletion; a
  Cfap47-mutated mouse PMID:33472045 Abstract
  only (PMC7895902 full text not retrievable through PubMed tools).
• Further MMAF/OAT families: PMID:37424856 (p.V472M; head, mitochondrial sheath and
  annulus defects; co-IP with SEPTIN4, CFAP65, CFAP69) and PMID:36571501 (abstract only;
  CFAP47 interacts with WDR87 in the midpiece).
• Airway: PMID:37723893 Respiratory cilia were short and fewer but
  the 9+2 structure was intact; the PCD association rests on two patients.
• Kidney (weaker): PMID:39698362; proposed X-linked PKD gene from three sporadic male patients.

Localization by immunofluorescence

• Two IF studies place a CFAP47 signal at the sperm head-tail junction:
  GOA IDA from PMID:33472045 (head-tail coupling apparatus; abstract only) and
  PMID:37723893
• This contrasts with its structural position along the central apparatus of the whole
  axoneme (PMID:40473901). A neck pool or epitope accessibility could explain the IF.

Annotation decisions (summary)

• sperm axoneme assembly (IBA, IMP) -> ACCEPT (structural core of CA bridge; KO hollow
  bridge).
• cilium assembly (IBA) -> TOO_GENERAL (entailed by sperm axoneme assembly).
• cilium (IBA) -> TOO_GENERAL, entailed by NEW axonemal central apparatus.
• NEW: axonemal central apparatus (GO:1990716). Comparator check: HYDIN (its bridge
  partner), SPAG16, SPAG17, CFAP65 and MYCBPAP carry GO:1990716 in human GOA.
• protein binding x3 (BioPlex UBB x2; CFAP65) -> REMOVE (uninformative).
• sperm head-tail coupling apparatus (IDA) -> KEEP_AS_NON_CORE.

Review round 2 (PR 5062 automated review): molecular function and comparator checks

Molecular function

The first pass removed the three protein binding rows and asserted no MF, leaving CFAP47
with no MF aspect. The in situ structure (PMID:40473901, full text) does support specific
activities, so two NEW MF rows were added:

• GO:0005200 structural constituent of cytoskeleton (enables; ISS from mouse Cfap47,
  MGI:MGI:3781475), also set as core_functions.molecular_function.
  PMID:40473901 and PMID:40473901 This follows the repository precedent for
  CFAP43 (genes/human/CFAP43/CFAP43-ai-review.yaml, NEW GO:0005200 enables from a native
  axoneme structure).
• GO:0008017 microtubule binding (enables; ISS from mouse Cfap47), a second core function.
  PMID:40473901 and PMID:40473901.
• Evidence code: the structure is of mouse sperm, so ISS with the mouse ortholog as the
  WITH/FROM entity, not IDA (CFAP43 was IDA because its structure was a native human
  axoneme). MGI:MGI:3781475 was confirmed as mouse Cfap47 (UniProt query
  gene_exact:Cfap47 AND organism_id:10090 returns A0A0G2JEB6 with MGI:3781475, run
  2026-10-16) and is the MGI id already in the CFAP47 GOA WITH/FROM for the IBA rows.
• The NEW GO:1990716 axonemal central apparatus row now has qualifier: part_of and
  supporting_entities: MGI:MGI:3781475.

Comparator checks (QuickGO annotation search, run 2026-10-16)

Query: https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId=UniProtKB:<acc>&goId=<term>&goUsage=exact.

• GO:1990716 axonemal central apparatus, human: HYDIN (Q4G0P3) ISS + IEA; SPAG16 (Q8N0X2)
  IBA + IEA; SPAG17 (Q6Q759) IBA + IEA; CFAP65 (Q6ZU64) ISS + IEA; MYCBPAP (Q8TBZ2) ISS.
  The claim in the review holds. CFAP47 (Q6ZTR5) itself has none.
• MF on central-apparatus proteins (aspect=molecular_function, excluding GO:0005515):
  HYDIN, SPAG6, SPAG16, SPAG17, SPEF2, CFAP46, CFAP54, CFAP74 carry no MF; CFAP65 only
  GO:0003723 (HDA); MYCBPAP only GO:0005543 and GO:0030276 (IBA). CFAP43 itself has no
  GO:0005200 in GOA yet (the precedent is a NEW proposal in this repository). So GOA has
  no convention for or against an MF on central-apparatus scaffolds; the absence reflects
  missing structural curation.
• GO:0008017 microtubule binding, human (goId=GO:0008017&taxonId=9606, all pages):
  axonemal/ciliary proteins carrying it include SPEF1 (IBA, ISS), CFAP144 (IDA), CFAP100
  (IMP), CFAP157 (IBA, IEA, ISS), SAXO1 (IBA, IDA, IEA), SAXO2 and SAXO6, DRC4 (IEA).
• GO:0005200 structural constituent of cytoskeleton, human: mainly tubulins, spectrins,
  ankyrins, talins; the only sperm-specific carriers are CYLC1/CYLC2 (calyx). No axonemal
  protein carries it in GOA.

CFAP65 protein-binding row

Its own source (PMID:33472045) is abstract-only here and the abstract does not describe
the interaction; the reason now says so, and distinguishes this targeted assay from the
two BioPlex AP-MS rows. The quote is from the independent co-IP study PMID:37424856.