Is CFAP210 p.Ala196Thr (c.586G>A) pathogenic?

CFAP210 p.Ala196Thr (c.586G>A) is classified Uncertain significance in CFAP210 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-16). Rare (popmax 0.397%, mid).

How common is CFAP210 p.Ala196Thr (c.586G>A) in the general population?

CFAP210 p.Ala196Thr (c.586G>A) is rare (popmax 0.397%, mid) (gnomAD).

CFAP210 p.Ala196Thr

c.586G>A · rs200589066 · VCV2454657

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.397%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.211	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.7	GERP 1.9, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 48 kb · p 0.24 · regional, not allelic
Overall
CADD	23.9	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.397% Middle Eastern · 24/6,050 alleles

Filtering AF 0.273% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.233%

Overall 0.0757% 1,218/1,609,242 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.778%	128
Middle Easterngrpmax	0.397%	252
South Asian	0.155%	644
Remaining individualsnot grpmax-eligible	0.12%	830
European (non-Finnish)	0.0593%	1,687
Finnishnot grpmax-eligible	0.0424%	2,360
Admixed American	0.0272%	3,681
African / African-American	0.0107%	9,335

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Ala196Thr
Coding: c.586G>A
MANE Select: NM_001085447
dbSNP: rs200589066
Type: single nucleotide variant
Location: chr2:169674652 (GRCh38)
Structure: AlphaFold pLDDT 81.20 · 2 PDB
Residue 196: the trichohyalin-plectin-homology domain

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

Similar variants

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
CFAP210 p.Arg111His Uncertain significance ★ same type
CFAP210 p.Arg134Lys 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-ala196thr (accessed [today's date]).

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