Is CFAP119 p.Arg279Gln (c.836G>A) pathogenic?

CFAP119 p.Arg279Gln (c.836G>A) is classified Benign in CFAP119 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-01). AlphaMissense: likely benign (0.0672); Low-frequency (popmax 1.05%, sas).

How common is CFAP119 p.Arg279Gln (c.836G>A) in the general population?

CFAP119 p.Arg279Gln (c.836G>A) is low-frequency (popmax 1.05%, sas) (gnomAD).

What do computational predictors say about CFAP119 p.Arg279Gln (c.836G>A)?

AlphaMissense predicts likely benign (score 0.0672) — an in-silico prediction, not a clinical call.

CFAP119 p.Arg279Gln

c.836G>A · rs201418865 · VCV2646415

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0672 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.05%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0672	likely benign
REVEL	0.044	moderately benign-leaning
SaProt	LLR -4.27	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 -1.8	GERP -3.3
Regional constraint	o/e 1.02	unconstrained · MANE · 4,269 bp · p 0.72 · regional, not allelic
Overall
CADD	4.093	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 1.05% South Asian · 955/90,978 alleles

Filtering AF 0.994% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.972%

Overall 0.0681% 1,099/1,613,254 alleles · low-frequency

Ancestry group	Frequency	1 in
South Asiangrpmax	1.05%	95
Remaining individualsnot grpmax-eligible	0.0736%	1,358
Middle Eastern	0.0165%	6,050
European (non-Finnish)	0.00763%	13,105
East Asian	0.00669%	14,951
Finnishnot grpmax-eligible	0.00313%	31,988
Admixed American	0.00167%	59,940
African / African-American	0.00133%	75,040

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.Arg279Gln
Coding: c.836G>A
MANE Select: NM_001014979
dbSNP: rs201418865
Type: single nucleotide variant
Location: chr16:30757636 (GRCh38)
Structure: AlphaFold pLDDT 74.17

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-arg279gln (accessed [today's date]).

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