Is CFAP119 p.Arg317Gln (c.950G>A) pathogenic?

CFAP119 p.Arg317Gln (c.950G>A) is classified Likely benign in CFAP119 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-22). AlphaMissense: likely benign (0.0616); Very rare (popmax 0.00483%, nfe).

How common is CFAP119 p.Arg317Gln (c.950G>A) in the general population?

CFAP119 p.Arg317Gln (c.950G>A) is very rare (popmax 0.00483%, nfe) (gnomAD).

What do computational predictors say about CFAP119 p.Arg317Gln (c.950G>A)?

AlphaMissense predicts likely benign (score 0.0616) — an in-silico prediction, not a clinical call.

CFAP119 p.Arg317Gln

c.950G>A · rs572438853 · VCV3143320

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0616 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00483%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0616	likely benign
REVEL	0.033	moderately benign-leaning
SaProt	LLR -4.41	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 -3.7	GERP -5
Regional constraint	o/e 1.02	unconstrained · MANE · 4,269 bp · p 0.72 · regional, not allelic
Overall
CADD	0.41	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 0.00483% European (non-Finnish) · 57/1,180,006 alleles

Filtering AF 0.00377% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00345%

Overall 0.00372% 60/1,614,124 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00483%	20,702
South Asian	0.0022%	45,536
Remaining individualsnot grpmax-eligible	0.0016%	62,510

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: CFAP119
Protein: p.Arg317Gln
Coding: c.950G>A
MANE Select: NM_001014979
dbSNP: rs572438853
Type: single nucleotide variant
Location: chr16:30757522 (GRCh38)
Structure: AlphaFold pLDDT 74.17
Residue 317: the 'disordered' region

Full CFAP119 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP119 p.Ala118Thr Uncertain significance ★ ⚠ same type
CFAP119 p.Ala127Thr Uncertain significance ★ ⚠ same type
CFAP119 p.Ala143Val Uncertain significance ★ ⚠ same type
CFAP119 p.Ala196Ser Uncertain significance ★ ⚠ same type
CFAP119 p.Ala196Val Uncertain significance ★ ⚠ same type
CFAP119 p.Ala53Val Uncertain significance ★ ⚠ same type
CFAP119 p.Arg132Cys Uncertain significance ★ ⚠ same type
CFAP119 p.Arg181Trp 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/cfap119-p-arg317gln (accessed [today's date]).

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