OSR1 p.Pro115=
c.345G>T · rs45587636 · VCV723969
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.02%, 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 -10 | GERP -14 |
| Overall | ||
| CADD | 1.776 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.02%
African / African-American · 766/75,066 alleles
Filtering AF
0.961%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.937%
Overall
0.0532%
858/1,613,972 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.02% | 98 |
| Admixed American | 0.065% | 1,539 |
| Remaining individualsnot grpmax-eligible | 0.0592% | 1,689 |
| Middle Eastern | 0.0495% | 2,021 |
| South Asian | 0.00878% | 11,385 |
| 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
- OSR1
- Protein
- p.Pro115=
- Coding
- c.345G>T
- MANE Select
- NM_016470 · reported on NM_145260
- dbSNP
- rs45587636
- Type
- single nucleotide variant
- Location
- chr2:19353461 (GRCh38)
- Structure
- AlphaFold pLDDT 58.65
- Residue 115
- the 'disordered' region
Similar variants
- OSR1 p.Gly139= Likely benign ★★ same type
- OSR1 p.Leu218= Benign ★★ same type
- OSER1 p.Ala145Glu Uncertain significance ★ ⚠ same type
- OSER1 p.Ala145Thr Uncertain significance ★ ⚠ same type
- OSER1 p.Ala169Thr Uncertain significance ★ ⚠ same type
- OSER1 p.Ala57Val Uncertain significance ★ ⚠ same type
- OSER1 p.Arg230Gln Uncertain significance ★ ⚠ same type
- OSER1 p.Arg258Gln 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/osr1-p-pro115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown