Is CFAP210 p.Lys178Arg (c.533A>G) pathogenic?

CFAP210 p.Lys178Arg (c.533A>G) is classified Uncertain significance in CFAP210 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-19). Ultra-rare (popmax 0.0134%, eas).

How common is CFAP210 p.Lys178Arg (c.533A>G) in the general population?

CFAP210 p.Lys178Arg (c.533A>G) is ultra-rare (popmax 0.0134%, eas) (gnomAD).

CFAP210 p.Lys178Arg

c.533A>G · rs776324974 · VCV2619328

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.032	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP -2.1, phastCons 0.82
Regional constraint	o/e 0.95	unconstrained · MANE · 48 kb · p 0.24 · regional, not allelic
Overall
CADD	14.51	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% East Asian · 6/44,784 alleles

Filtering AF 0.0058% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00395%

Overall 0.000373% 6/1,608,980 alleles · ultra-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: CFAP210
Protein: p.Lys178Arg
Coding: c.533A>G
MANE Select: NM_001085447
dbSNP: rs776324974
Type: single nucleotide variant
Location: chr2:169674705 (GRCh38)
Structure: AlphaFold pLDDT 81.20 · 2 PDB
Residue 178: the trichohyalin-plectin-homology domain

Full CFAP210 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP210 p.Lys178Asn Uncertain significance ★ same residue
CFAP210 p.Ala196Thr Uncertain significance ★ same type
CFAP210 p.Ala349Gly Uncertain significance ★ same type
CFAP210 p.Ala372Gly Uncertain significance ★ same type
CFAP210 p.Ala382Val Uncertain significance ★ same type
CFAP210 p.Ala405Val Uncertain significance ★ same type
CFAP210 p.Ala446Glu Uncertain significance ★ same type
CFAP210 p.Ala462Thr 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/cfap210-p-lys178arg (accessed [today's date]).

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