OSMR p.Pro959=
c.2877C>G · rs190725368 · VCV3037356
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.588%, eas)
Conditions
1
OSMR-related disorder
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 -0.92 | GERP 0.007 |
| Overall | ||
| CADD | 0.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.588%
East Asian · 264/44,880 alleles
Filtering AF
0.53%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.507%
Overall
0.0172%
277/1,614,050 alleles · rare
exomes 255/1,461,780 · genomes 22/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.588% | 170 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,813 |
| Admixed American | 0.00167% | 60,016 |
| European (non-Finnish) | 0.000339% | 294,982 |
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.Pro959=
- Coding
- c.2877C>G
- MANE Select
- NM_003999
- dbSNP
- rs190725368
- Type
- single nucleotide variant
- Location
- chr5:38933381 (GRCh38)
- Gene constraint
- LOEUF 0.927 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.07 · 1 PDB
- Residue 959
- a UniProt-annotated variant site (in)
Disease context
OSMR-related disorder
Similar variants
- OSMR p.Ile691Thr Likely pathogenic ★★ ⚠ same condition
- OSMR p.Ile807Thr Uncertain significance ★★ ⚠ same condition
- OSMR c.991+40G>A Likely benign same condition
- OSMR p.Cys505= Likely benign same condition
- OSMR p.Glu527Lys Benign same condition
- OSMR p.His187Gln Benign same condition
- OSMR p.Leu569= Likely benign same condition
- OSMR p.Pro960= Likely benign same condition
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-pro959 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown