Is CFAP410 p.Ser59= (c.177C>T) pathogenic?

CFAP410 p.Ser59= (c.177C>T) is classified Likely benign in CFAP410 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-28). Very rare (popmax 0.004%, afr).

How common is CFAP410 p.Ser59= (c.177C>T) in the general population?

CFAP410 p.Ser59= (c.177C>T) is very rare (popmax 0.004%, afr) (gnomAD).

CFAP410 p.Ser59=

c.177C>T · rs1057356386 · VCV1134881

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.004%, 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 3.1	GERP 0.15, phastCons 1
Overall
CADD	14.1	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.004% African / African-American · 3/74,922 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000495%

Overall 0.000248% 4/1,612,408 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.004%	24,974
Remaining individualsnot grpmax-eligible	0.0016%	62,442

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: CFAP410
Protein: p.Ser59=
Coding: c.177C>T
MANE Select: NM_004928
dbSNP: rs1057356386
Type: single nucleotide variant
Location: chr21:44333229 (GRCh38)
Gene constraint: LOEUF 1.453 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.77 · 1 PDB

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

Similar variants

CFAP410 p.Ser59Cys Uncertain significance ★ ⚠ same residue
CFAP410 p.Ser59fs Pathogenic ★ 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

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-ser59 (accessed [today's date]).

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