OSMR p.Lys899=
c.2697A>G · VCV4970180
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.346%, mid)
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 -0.3 | GERP -3.4 |
| Overall | ||
| CADD | 1.703 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.346%
Middle Eastern · 21/6,062 alleles
Filtering AF
0.232%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.195%
Overall
0.0343%
554/1,614,198 alleles · rare
exomes 399/1,461,882 · genomes 155/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.346% | 289 |
| Admixed American | 0.155% | 645 |
| African / African-American | 0.152% | 658 |
| Ashkenazi Jewishnot grpmax-eligible | 0.098% | 1,021 |
| Remaining individualsnot grpmax-eligible | 0.088% | 1,137 |
| European (non-Finnish) | 0.0205% | 4,876 |
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.Lys899=
- Coding
- c.2697A>G
- MANE Select
- NM_003999
- Type
- single nucleotide variant
- Location
- chr5:38933201 (GRCh38)
- Gene constraint
- LOEUF 0.927 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.07 · 1 PDB
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-lys899 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown