OSMR p.Ala508=
c.1524C>T · rs186633949 · VCV734898
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.168%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.12 | GERP -2.6, phastCons 0.022 |
| Overall | ||
| CADD | 0.904 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.168%
African / African-American · 126/74,896 alleles
Filtering AF
0.144%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.135%
Overall
0.00855%
138/1,613,994 alleles · rare
exomes 76/1,461,846 · genomes 62/152,148 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.168% | 594 |
| Middle Eastern | 0.0164% | 6,084 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,927 |
| Admixed American | 0.005% | 20,001 |
| European (non-Finnish) | 8.47e-05% | 1,180,011 |
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
- OSMR
- Protein
- p.Ala508=
- Coding
- c.1524C>T
- MANE Select
- NM_003999
- dbSNP
- rs186633949
- Type
- single nucleotide variant
- Location
- chr5:38919001 (GRCh38)
- Gene constraint
- LOEUF 0.927 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.07 · 1 PDB
- Residue 508
- the fibronectin type-iii 2 domain
Similar variants
- OSMR p.Ile691Thr Likely pathogenic ★★ ⚠ same type
- OSMR p.Pro694Leu Pathogenic/Likely pathogenic ★★ ⚠ same type
- OSMR p.Ile807Thr Uncertain significance ★★ ⚠ same type
- OSMR p.Ser866Ala Uncertain significance ★★ ⚠ same type
- OSMR p.Val662Ala Uncertain significance ★★ same type
- OSMR p.Ala950Glu Benign/Likely benign ★★ same type
- OSMR p.Glu388Lys Benign ★★ same type
- OSMR p.Ser800Thr Likely benign ★★ 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/osmr-p-ala508 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown