Is CFAP410 p.Cys61Gly (c.181T>G) pathogenic?

CFAP410 p.Cys61Gly (c.181T>G) is classified Uncertain significance in CFAP410 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). AlphaMissense: likely pathogenic (0.848); Absent from gnomAD v4.1.

How common is CFAP410 p.Cys61Gly (c.181T>G) in the general population?

CFAP410 p.Cys61Gly (c.181T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CFAP410 p.Cys61Gly (c.181T>G)?

AlphaMissense predicts likely pathogenic (score 0.848) — an in-silico prediction, not a clinical call.

CFAP410 p.Cys61Gly

c.181T>G · rs2047686233 · VCV863248

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.848 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.848	likely pathogenic
REVEL	0.605	indeterminate
SaProt	LLR -15.16	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.3, phastCons 1
Regional constraint	o/e 1.21	unconstrained · MANE · 8,993 bp · p 8.7e-05 · regional, not allelic
Overall
CADD	28.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CFAP410
Protein: p.Cys61Gly
Coding: c.181T>G
MANE Select: NM_004928
dbSNP: rs2047686233
Type: single nucleotide variant
Location: chr21:44333225 (GRCh38)
Gene constraint: LOEUF 1.453 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.77 · 1 PDB
Residue 61: a UniProt-annotated variant site (in rdms)

Full CFAP410 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP410 p.Cys61Tyr Uncertain significance ★ ⚠ same residue
CFAP410 c.545+1G>A Pathogenic ★★ same type
CFAP410 c.642+2T>C Pathogenic ★★ same type
CFAP410 c.643-1G>C Pathogenic ★★ same type
CFAP410 c.643-23A>T Pathogenic/Likely pathogenic ★★ same type
CFAP410 c.96+1G>A Pathogenic ★★ same type
CFAP410 c.96+1G>T Pathogenic/Likely pathogenic ★★ same type
CFAP410 p.Arg73Pro Pathogenic/Likely pathogenic ★★ ⚠ 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/cfap410-p-cys61gly (accessed [today's date]).

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