Is CFAP119 p.Ala143Val (c.428C>T) pathogenic?

CFAP119 p.Ala143Val (c.428C>T) is classified Uncertain significance in CFAP119 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-25). AlphaMissense: likely benign (0.1357); Ultra-rare (popmax 0.0296%, sas).

How common is CFAP119 p.Ala143Val (c.428C>T) in the general population?

CFAP119 p.Ala143Val (c.428C>T) is ultra-rare (popmax 0.0296%, sas) (gnomAD).

What do computational predictors say about CFAP119 p.Ala143Val (c.428C>T)?

AlphaMissense predicts likely benign (score 0.1357) — an in-silico prediction, not a clinical call.

CFAP119 p.Ala143Val

c.428C>T · VCV3266387

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1357 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0296%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1357	likely benign
REVEL	0.166	moderately benign-leaning
SaProt	LLR -8.88	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 5.2	GERP 1.2, phastCons 0.98
Regional constraint	o/e 1.02	unconstrained · MANE · 4,269 bp · p 0.72 · regional, not allelic
Overall
CADD	19.68	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0296% South Asian · 27/91,088 alleles

Filtering AF 0.0208% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.018%

Overall 0.00204% 33/1,614,214 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0296%	3,374
Remaining individualsnot grpmax-eligible	0.0032%	31,253
European (non-Finnish)	0.000339%	295,010

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.Ala143Val
Coding: c.428C>T
MANE Select: NM_001014979
Type: single nucleotide variant
Location: chr16:30760325 (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.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
CFAP119 p.Arg207His 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-ala143val (accessed [today's date]).

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