CD200 p.Leu113Pro
c.338T>C · VCV3998078
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, eas)
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 4.8 | GERP 1.9, phastCons 1 |
| Regional constraint | o/e 0.81 | unconstrained · MANE · 28 kb · p 0.00055 · regional, not allelic |
| Overall | ||
| CADD | 23.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
East Asian · 6/44,896 alleles
Filtering AF
0.00579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00394%
Overall
0.000434%
7/1,614,006 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0134% | 7,483 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
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.Leu113Pro
- Coding
- c.338T>C
- MANE Select
- NM_005944
- Type
- single nucleotide variant
- Location
- chr3:112345205 (GRCh38)
- Gene constraint
- LOEUF 0.85 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 86.39
- Residue 113
- a disulfide bond; the ig-like v-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-leu113pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown