Is CFAP210 p.Ile397Val (c.1189A>G) pathogenic?

CFAP210 p.Ile397Val (c.1189A>G) is classified Uncertain significance in CFAP210 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-03). Very rare (popmax 0.000593%, nfe).

How common is CFAP210 p.Ile397Val (c.1189A>G) in the general population?

CFAP210 p.Ile397Val (c.1189A>G) is very rare (popmax 0.000593%, nfe) (gnomAD).

CFAP210 p.Ile397Val

c.1189A>G · rs2528403227 · VCV3143372

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000593%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.052	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.96	GERP -1.1, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 48 kb · p 0.24 · regional, not allelic
Overall
CADD	15.5	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000593% European (non-Finnish) · 7/1,179,622 alleles

Filtering AF 0.000247% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000159%

Overall 0.000479% 7/1,460,274 alleles · very 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.Ile397Val
Coding: c.1189A>G
MANE Select: NM_001085447
dbSNP: rs2528403227
Type: single nucleotide variant
Location: chr2:169649310 (GRCh38)
Structure: AlphaFold pLDDT 81.20 · 2 PDB
Residue 397: the trichohyalin-plectin-homology domain

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

Similar variants

CFAP210 p.Ile397Arg 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-ile397val (accessed [today's date]).

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