OSTM1 p.Ala92=
c.276C>G · rs2482241827 · VCV2702449
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.54e-05%, nfe)
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 2.8 | GERP 0.55, phastCons 1 |
| Overall | ||
| CADD | 11.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.54e-05%
European (non-Finnish) · 1/1,170,494 alleles
Overall
6.27e-05%
1/1,593,656 alleles · very rare
exomes 1/1,441,322 · genomes 0/152,334 · joint denominator
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
- OSTM1
- Protein
- p.Ala92=
- Coding
- c.276C>G
- MANE Select
- NM_014028
- dbSNP
- rs2482241827
- Type
- single nucleotide variant
- Location
- chr6:108074376 (GRCh38)
- Gene constraint
- LOEUF 1.425 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.62 · 9 PDB
- Residue 92
- an α-helix
Similar variants
- OSTM1 p.Arg266Ter Pathogenic/Likely pathogenic ★★ same type
- OSTM1 c.*147G>T Uncertain significance ★★ same type
- OSTM1 c.*2362A>G Uncertain significance ★★ same type
- OSTM1 p.Arg144Lys Uncertain significance ★★ ⚠ same type
- OSTM1 p.Arg225Cys Uncertain significance ★★ ⚠ same type
- OSTM1 p.Arg225His Uncertain significance ★★ ⚠ same type
- OSTM1 p.Arg85Pro Uncertain significance ★★ ⚠ same type
- OSTM1 p.Asn246Ser 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/ostm1-p-ala92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown