Is CFAP47 p.Arg574His (c.1721G>A) pathogenic?

CFAP47 p.Arg574His (c.1721G>A) is classified Likely benign in CFAP47 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-01). AlphaMissense: likely benign (0.0711); Ultra-rare (popmax 0.0229%, mid).

How common is CFAP47 p.Arg574His (c.1721G>A) in the general population?

CFAP47 p.Arg574His (c.1721G>A) is ultra-rare (popmax 0.0229%, mid) (gnomAD).

What do computational predictors say about CFAP47 p.Arg574His (c.1721G>A)?

AlphaMissense predicts likely benign (score 0.0711) — an in-silico prediction, not a clinical call.

CFAP47 p.Arg574His

c.1721G>A · VCV4533838

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0711 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0229%, mid)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.0711	likely benign
REVEL	0.036	moderately 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 -2.2	GERP -3.1
Regional constraint	o/e 1.10	unconstrained · MANE · 465 kb · p 2.3e-05 · regional, not allelic
Overall
CADD	0.013	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 0.0229% Middle Eastern · 1/4,359 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000858%

Overall 0.00158% 19/1,206,279 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0229%	4,359
East Asian	0.00297%	33,667
European (non-Finnish)	0.00179%	55,821
African / African-American	0.00176%	56,673

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.Arg574His
Coding: c.1721G>A
MANE Select: NM_001304548
Type: single nucleotide variant
Location: chrX:35967739 (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-arg574his (accessed [today's date]).

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