CD200 p.Pro238Leu
c.713C>T · rs1247915689 · VCV2559063
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00268%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.323 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.4 | GERP 1.7, phastCons 1 |
| Regional constraint | o/e 0.81 | unconstrained · MANE · 28 kb · p 0.00055 · regional, not allelic |
| Overall | ||
| CADD | 27.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00268%
African / African-American · 2/74,684 alleles
Filtering AF
0.000444%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000373%
6/1,610,602 alleles · very rare
exomes 4/1,458,612 · genomes 2/151,990 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00268% | 37,342 |
| East Asian | 0.00224% | 44,708 |
| South Asian | 0.00111% | 90,414 |
| European (non-Finnish) | 0.00017% | 589,168 |
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.Pro238Leu
- Coding
- c.713C>T
- MANE Select
- NM_005944
- dbSNP
- rs1247915689
- Type
- single nucleotide variant
- Location
- chr3:112349730 (GRCh38)
- Gene constraint
- LOEUF 0.85 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 86.39
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-pro238leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown