Is CD200 p.Ala23Val (c.68C>T) pathogenic?

CD200 p.Ala23Val (c.68C>T) is classified Uncertain significance in CD200 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-06). Ultra-rare (popmax 0.0329%, mid).

How common is CD200 p.Ala23Val (c.68C>T) in the general population?

CD200 p.Ala23Val (c.68C>T) is ultra-rare (popmax 0.0329%, mid) (gnomAD).

CD200 p.Ala23Val

c.68C>T · rs756780987 · VCV3140409

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0329%, mid)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.075	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.2	GERP 0.92, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 28 kb · p 0.00055 · regional, not allelic
Overall
CADD	17.56	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0329% Middle Eastern · 2/6,080 alleles

Filtering AF 0.0058% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00241%

Overall 0.00192% 31/1,612,030 alleles · ultra-rare exomes 29/1,459,862 · genomes 2/152,168 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0329%	3,040
Remaining individualsnot grpmax-eligible	0.0032%	31,215
European (non-Finnish)	0.00229%	43,639

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: CD200
Protein: p.Ala23Val
Coding: c.68C>T
MANE Select: NM_005944
dbSNP: rs756780987
Type: single nucleotide variant
Location: chr3:112340957 (GRCh38)
Gene constraint: LOEUF 0.85 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 86.39

Full CD200 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD200 c.12+2787T>A Uncertain significance ★ same type
CD200 p.Arg261His Uncertain significance ★ same type
CD200 p.Arg3Thr Uncertain significance ★ same type
CD200 p.Asn157Ser Uncertain significance ★ same type
CD200 p.Asn55Lys Uncertain significance ★ same type
CD200 p.Asn81Lys Uncertain significance ★ same type
CD200 p.Gln42His Uncertain significance ★ same type
CD200 p.Glu41Gln 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/cd200-p-ala23val (accessed [today's date]).

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