STN1 p.Val293=
c.879A>T · VCV3692935
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.5e-05%, nfe)
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 0.11 | GERP 0.41, phastCons 0.99 |
| Overall | ||
| CADD | 8.763 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.5e-05%
European (non-Finnish) · 1/1,176,656 alleles
Overall
6.21e-05%
1/1,610,444 alleles · very rare
exomes 1/1,458,112 · genomes 0/152,332 · 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
- STN1
- Protein
- p.Val293=
- Coding
- c.879A>T
- MANE Select
- NM_024928
- Type
- single nucleotide variant
- Location
- chr10:103889142 (GRCh38)
- Gene constraint
- LOEUF 0.975 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.67 · 8 PDB
- Residue 293
- the 'winged helix-turn-helix (whth) 1' region; a β-strand
Similar variants
- STN1 p.Ala192Thr Uncertain significance ★★ ⚠ same type
- STN1 p.Ala262Glu Uncertain significance ★★ ⚠ same type
- STN1 p.Ala262Thr Uncertain significance ★★ ⚠ same type
- STN1 p.Ala367Val Uncertain significance ★★ ⚠ same type
- STN1 p.Arg133Gln Uncertain significance ★★ ⚠ same type
- STN1 p.Arg295Gly Uncertain significance ★★ ⚠ same type
- STN1 p.Arg306Trp Uncertain significance ★★ ⚠ same type
- STN1 p.Arg332Cys 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/stn1-p-val293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown