Is CD200 p.Pro189Thr (c.565C>A) pathogenic?

CD200 p.Pro189Thr (c.565C>A) is classified Uncertain significance in CD200 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-29). Very rare (popmax 0.00446%, eas).

How common is CD200 p.Pro189Thr (c.565C>A) in the general population?

CD200 p.Pro189Thr (c.565C>A) is very rare (popmax 0.00446%, eas) (gnomAD).

CD200 p.Pro189Thr

c.565C>A · rs772898326 · VCV2531079

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00446%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.008	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.51	GERP -0.98
Regional constraint	o/e 0.81	unconstrained · MANE · 28 kb · p 0.00055 · regional, not allelic
Overall
CADD	13.38	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00446% East Asian · 2/44,890 alleles

Filtering AF 0.000739% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000276%

Overall 0.000124% 2/1,613,876 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: CD200
Protein: p.Pro189Thr
Coding: c.565C>A
MANE Select: NM_005944
dbSNP: rs772898326
Type: single nucleotide variant
Location: chr3:112347701 (GRCh38)
Gene constraint: LOEUF 0.85 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 86.39
Residue 189: a disulfide bond; the ig-like c2-type domain

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.Ala23Val 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

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-pro189thr (accessed [today's date]).

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