Is CFAP97 p.Glu11Gln (c.31G>C) pathogenic?

CFAP97 p.Glu11Gln (c.31G>C) is classified Uncertain significance in CFAP97 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-07). AlphaMissense: likely pathogenic (0.6942); Ultra-rare (popmax 0.0671%, eas).

How common is CFAP97 p.Glu11Gln (c.31G>C) in the general population?

CFAP97 p.Glu11Gln (c.31G>C) is ultra-rare (popmax 0.0671%, eas) (gnomAD).

What do computational predictors say about CFAP97 p.Glu11Gln (c.31G>C)?

AlphaMissense predicts likely pathogenic (score 0.6942) — an in-silico prediction, not a clinical call.

CFAP97 p.Glu11Gln

c.31G>C · VCV4653009

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6942 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0671%, eas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.6942	likely pathogenic
REVEL	0.502	indeterminate
SaProt	LLR -9.72	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.40 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 28 kb · p 0.14 · regional, not allelic
Overall
CADD	24.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0671% East Asian · 30/44,704 alleles

Filtering AF 0.0483% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0419%

Overall 0.00389% 62/1,593,680 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0671%	1,490
Remaining individualsnot grpmax-eligible	0.0275%	3,635
South Asian	0.0136%	7,335
Admixed American	0.00175%	57,176
European (non-Finnish)	0.000171%	586,414

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CFAP97
Protein: p.Glu11Gln
Coding: c.31G>C
MANE Select: NM_020827
Type: single nucleotide variant
Location: chr4:185191166 (GRCh38)
Gene constraint: LOEUF 1.095 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 58.55

Full CFAP97 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP97 p.Glu383= Benign ★★ same type
CFAP97 p.Thr499Met Benign ★★ same type
CFAP97 p.Ala152Gly Uncertain significance ★ ⚠ same type
CFAP97 p.Ala448Thr Uncertain significance ★ ⚠ same type
CFAP97 p.Arg381Ser Uncertain significance ★ ⚠ same type
CFAP97 p.Arg389Gln Uncertain significance ★ ⚠ same type
CFAP97 p.Arg457His Uncertain significance ★ ⚠ same type
CFAP97 p.Arg479Trp Uncertain significance ★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cfap97-p-glu11gln (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown