Is CFAP61 p.Arg124= (c.372A>C) pathogenic?

CFAP61 p.Arg124= (c.372A>C) is classified Likely benign in CFAP61 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-22). Rare (popmax 0.517%, afr).

How common is CFAP61 p.Arg124= (c.372A>C) in the general population?

CFAP61 p.Arg124= (c.372A>C) is rare (popmax 0.517%, afr) (gnomAD).

CFAP61 p.Arg124=

c.372A>C · VCV4227108

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.517%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 0.18, phastCons 1
Overall
CADD	13.79	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.517% African / African-American · 388/74,990 alleles

Filtering AF 0.475% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.458%

Overall 0.0269% 434/1,613,994 alleles · rare exomes 221/1,461,816 · genomes 213/152,178 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.517%	193
Remaining individualsnot grpmax-eligible	0.0432%	2,315
Admixed American	0.0217%	4,616
European (non-Finnish)	0.000509%	196,656

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: CFAP61
Protein: p.Arg124=
Coding: c.372A>C
MANE Select: NM_015585
Type: single nucleotide variant
Location: chr20:20075189 (GRCh38)
Gene constraint: LOEUF 0.892 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.86 · 1 PDB

Full CFAP61 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP61 p.Arg552Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
CFAP61 c.3125-1G>C Likely pathogenic ★ same type
CFAP61 p.Arg283Ter Pathogenic ★ same type
CFAP61 p.Val755Ala Likely pathogenic ★ ⚠ same type
CFAP61 p.Ala1026Asp Uncertain significance ★ ⚠ same type
CFAP61 p.Ala1081Gly Uncertain significance ★ ⚠ same type
CFAP61 p.Ala1081Ser Uncertain significance ★ ⚠ same type
CFAP61 p.Ala1232Val 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/cfap61-p-arg124 (accessed [today's date]).

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