Is CFAP119 p.Glu305Lys (c.913G>A) pathogenic?

CFAP119 p.Glu305Lys (c.913G>A) is classified Uncertain significance in CFAP119 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-05). AlphaMissense: likely benign (0.2179); Ultra-rare (popmax 0.0164%, mid).

How common is CFAP119 p.Glu305Lys (c.913G>A) in the general population?

CFAP119 p.Glu305Lys (c.913G>A) is ultra-rare (popmax 0.0164%, mid) (gnomAD).

What do computational predictors say about CFAP119 p.Glu305Lys (c.913G>A)?

AlphaMissense predicts likely benign (score 0.2179) — an in-silico prediction, not a clinical call.

CFAP119 p.Glu305Lys

c.913G>A · VCV4226825

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2179 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0164%, mid)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2179	likely benign
REVEL	0.243	benign-leaning
SaProt	LLR -12.10	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.3	GERP 2.5, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 4,269 bp · p 0.72 · regional, not allelic
Overall
CADD	24.7	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 0.0164% Middle Eastern · 1/6,082 alleles

Filtering AF 0.00751% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00593%

Overall 0.00229% 37/1,614,112 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0164%	6,082
South Asian	0.0132%	7,591
Finnishnot grpmax-eligible	0.00625%	16,010
East Asian	0.00445%	22,450
Remaining individualsnot grpmax-eligible	0.0016%	62,490
European (non-Finnish)	0.00136%	73,753
African / African-American	0.00133%	74,942

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.Glu305Lys
Coding: c.913G>A
MANE Select: NM_001014979
Type: single nucleotide variant
Location: chr16:30757559 (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-glu305lys (accessed [today's date]).

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