Is CFAP47 p.Ile325Phe (c.973A>T) pathogenic?

CFAP47 p.Ile325Phe (c.973A>T) is classified Uncertain significance in CFAP47 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-06-18). AlphaMissense: likely benign (0.1613); Very rare (popmax 0.00182%, afr).

How common is CFAP47 p.Ile325Phe (c.973A>T) in the general population?

CFAP47 p.Ile325Phe (c.973A>T) is very rare (popmax 0.00182%, afr) (gnomAD).

What do computational predictors say about CFAP47 p.Ile325Phe (c.973A>T)?

AlphaMissense predicts likely benign (score 0.1613) — an in-silico prediction, not a clinical call.

CFAP47 p.Ile325Phe

c.973A>T · rs1173398550 · VCV2233338

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1613 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00182%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.1613	likely benign
REVEL	0.285	benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.2	GERP 0.33, phastCons 1
Regional constraint	o/e 1.10	unconstrained · MANE · 465 kb · p 2.3e-05 · regional, not allelic
Overall
CADD	15.15	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 0.00182% African / African-American · 1/54,868 alleles

Overall 0.000892% 1/112,093 alleles · very 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: CFAP47
Protein: p.Ile325Phe
Coding: c.973A>T
MANE Select: NM_001304548
dbSNP: rs1173398550
Type: single nucleotide variant
Location: chrX:35951890 (GRCh38)

Full CFAP47 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP47 p.Ser964Gly Uncertain significance ★★ same type
CFAP47 p.Thr2847Met Likely benign ★★ same type
CFAP47 c.3652-4G>C Uncertain significance ★ same type
CFAP47 p.Ala566Ser Uncertain significance ★ ⚠ same type
CFAP47 p.Arg429Cys Uncertain significance ★ ⚠ same type
CFAP47 p.Asp1565Val Uncertain significance ★ ⚠ same type
CFAP47 p.Gln2891His Uncertain significance ★ ⚠ same type
CFAP47 p.Gln439Pro 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/cfap47-p-ile325phe (accessed [today's date]).

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