Is CFAP184 p.Pro117Thr (c.349C>A) pathogenic?

CFAP184 p.Pro117Thr (c.349C>A) is classified Uncertain significance in CFAP184 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-08). AlphaMissense: likely benign (0.07); Ultra-rare (popmax 0.0553%, amr).

How common is CFAP184 p.Pro117Thr (c.349C>A) in the general population?

CFAP184 p.Pro117Thr (c.349C>A) is ultra-rare (popmax 0.0553%, amr) (gnomAD).

What do computational predictors say about CFAP184 p.Pro117Thr (c.349C>A)?

AlphaMissense predicts likely benign (score 0.07) — an in-silico prediction, not a clinical call.

CFAP184 p.Pro117Thr

c.349C>A · VCV3491196

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.07 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0553%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.07	likely benign
REVEL	0.028	moderately benign-leaning
SaProt	LLR -6.36	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 -2.4
Regional constraint	o/e 1.14	unconstrained · MANE · 1,664 bp · p 0.00013 · regional, not allelic
Overall
CADD	3.835	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 0.0553% Admixed American · 28/50,634 alleles

Filtering AF 0.0393% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0339%

Overall 0.00182% 28/1,537,328 alleles · ultra-rare

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.Pro117Thr
Coding: c.349C>A
MANE Select: NM_153376
Type: single nucleotide variant
Location: chr4:7042590 (GRCh38)
Structure: AlphaFold pLDDT 69.36 · 1 PDB
Residue 117: 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.Ala142Val 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

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-pro117thr (accessed [today's date]).

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