Is CFAP184 p.Ala142Val (c.425C>T) pathogenic?

CFAP184 p.Ala142Val (c.425C>T) is classified Uncertain significance in CFAP184 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-14). AlphaMissense: likely benign (0.101); Ultra-rare (popmax 0.0659%, mid).

How common is CFAP184 p.Ala142Val (c.425C>T) in the general population?

CFAP184 p.Ala142Val (c.425C>T) is ultra-rare (popmax 0.0659%, mid) (gnomAD).

What do computational predictors say about CFAP184 p.Ala142Val (c.425C>T)?

AlphaMissense predicts likely benign (score 0.101) — an in-silico prediction, not a clinical call.

CFAP184 p.Ala142Val

c.425C>T · rs202179693 · VCV2368929

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.101 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0659%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.101	likely benign
REVEL	0.007	strongly benign-leaning
SaProt	LLR -5.88	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 -1.7	GERP -2.8
Regional constraint	o/e 1.14	unconstrained · MANE · 1,664 bp · p 0.00013 · regional, not allelic
Overall
CADD	0.316	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 0.0659% Middle Eastern · 4/6,068 alleles

Filtering AF 0.0224% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0135%

Overall 0.00629% 101/1,605,308 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0659%	1,517
Ashkenazi Jewishnot grpmax-eligible	0.0373%	2,679
South Asian	0.00989%	10,107
Admixed American	0.00671%	14,894
Remaining individualsnot grpmax-eligible	0.00644%	15,536
European (non-Finnish)	0.00561%	17,834
African / African-American	0.00267%	37,393
Finnishnot grpmax-eligible	0.00168%	59,534

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: CFAP184
Protein: p.Ala142Val
Coding: c.425C>T
MANE Select: NM_153376
dbSNP: rs202179693
Type: single nucleotide variant
Location: chr4:7042514 (GRCh38)
Structure: AlphaFold pLDDT 69.36 · 1 PDB
Residue 142: the 'disordered' region

Full CFAP184 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP184 p.Ala105Thr Uncertain significance ★ ⚠ same type
CFAP184 p.Ala109Asp Uncertain significance ★ ⚠ same type
CFAP184 p.Ala126Thr Uncertain significance ★ ⚠ same type
CFAP184 p.Ala126Val Uncertain significance ★ ⚠ same type
CFAP184 p.Ala160Thr Uncertain significance ★ ⚠ same type
CFAP184 p.Ala275Ser Uncertain significance ★ ⚠ same type
CFAP184 p.Ala374Pro Uncertain significance ★ ⚠ same type
CFAP184 p.Ala469Val 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/cfap184-p-ala142val (accessed [today's date]).

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