Is CFAP157 p.Val29Met (c.85G>A) pathogenic?

CFAP157 p.Val29Met (c.85G>A) is classified Likely benign in CFAP157 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-19). AlphaMissense: likely benign (0.0846); Ultra-rare (popmax 0.0472%, sas).

How common is CFAP157 p.Val29Met (c.85G>A) in the general population?

CFAP157 p.Val29Met (c.85G>A) is ultra-rare (popmax 0.0472%, sas) (gnomAD).

What do computational predictors say about CFAP157 p.Val29Met (c.85G>A)?

AlphaMissense predicts likely benign (score 0.0846) — an in-silico prediction, not a clinical call.

CFAP157 p.Val29Met

c.85G>A · VCV3266393

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0846 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0472%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0846	likely benign
REVEL	0.021	moderately benign-leaning
SaProt	LLR -8.43	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.1	GERP -3.5
Regional constraint	o/e 0.92	unconstrained · MANE · 6,870 bp · p 0.054 · regional, not allelic
Overall
CADD	0.06	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 0.0472% South Asian · 43/91,080 alleles

Filtering AF 0.036% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0321%

Overall 0.00601% 97/1,613,726 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0472%	2,118
East Asian	0.0401%	2,491
African / African-American	0.00799%	12,509
Remaining individualsnot grpmax-eligible	0.0064%	15,627
Finnishnot grpmax-eligible	0.00314%	31,826
European (non-Finnish)	0.00203%	49,166

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: CFAP157
Protein: p.Val29Met
Coding: c.85G>A
MANE Select: NM_001012502
Type: single nucleotide variant
Location: chr9:127707116 (GRCh38)
Gene constraint: LOEUF 0.998 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.75

Full CFAP157 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP157 p.Ala121Val Uncertain significance ★ ⚠ same type
CFAP157 p.Ala365Val Uncertain significance ★ ⚠ same type
CFAP157 p.Ala420Glu Uncertain significance ★ ⚠ same type
CFAP157 p.Arg155Gln Uncertain significance ★ ⚠ same type
CFAP157 p.Arg155Trp Uncertain significance ★ ⚠ same type
CFAP157 p.Arg308His Uncertain significance ★ ⚠ same type
CFAP157 p.Arg317Thr Uncertain significance ★ ⚠ same type
CFAP157 p.Arg348Trp 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/cfap157-p-val29met (accessed [today's date]).

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