CD200 p.Phe151Leu
c.453C>A · rs202184567 · VCV2218615
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.354%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.02 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.059 | GERP -3.2, phastCons 0.19 |
| Regional constraint | o/e 0.81 | unconstrained · MANE · 28 kb · p 0.00055 · regional, not allelic |
| Overall | ||
| CADD | 2.075 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.354%
East Asian · 159/44,886 alleles
Filtering AF
0.309%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.292%
Overall
0.0104%
168/1,613,932 alleles · rare
exomes 160/1,461,688 · genomes 8/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.354% | 282 |
| Middle Eastern | 0.0165% | 6,058 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,250 |
| African / African-American | 0.00133% | 75,002 |
| European (non-Finnish) | 0.000424% | 235,970 |
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.Phe151Leu
- Coding
- c.453C>A
- MANE Select
- NM_005944
- dbSNP
- rs202184567
- Type
- single nucleotide variant
- Location
- chr3:112347589 (GRCh38)
- Gene constraint
- LOEUF 0.85 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 86.39
- Residue 151
- the ig-like c2-type domain
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-phe151leu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown