OSMR p.Pro960=
c.2880G>A · rs764796970 · VCV3053615
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, amr)
Conditions
1
OSMR-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.3 | GERP -3.1 |
| Overall | ||
| CADD | 0.764 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
Admixed American · 20/59,986 alleles
Filtering AF
0.0221%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0184%
Overall
0.0039%
63/1,613,796 alleles · ultra-rare
exomes 47/1,461,796 · genomes 16/152,000 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0333% | 2,999 |
| South Asian | 0.0198% | 5,058 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,943 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,600 |
| African / African-American | 0.00267% | 37,431 |
| East Asian | 0.00223% | 44,892 |
| European (non-Finnish) | 0.00102% | 98,326 |
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.Pro960=
- Coding
- c.2880G>A
- MANE Select
- NM_003999
- dbSNP
- rs764796970
- Type
- single nucleotide variant
- Location
- chr5:38933384 (GRCh38)
- Gene constraint
- LOEUF 0.927 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.07 · 1 PDB
Disease context
OSMR-related disorder
Similar variants
- OSMR p.Pro960Leu Likely benign ★ same residue
- 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
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-pro960 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown