STN1 p.Pro337=
c.1011G>A · rs756692794 · VCV721378
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00833%, amr)
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 -12 | GERP -3.9 |
| Overall | ||
| CADD | 1.921 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/59,994 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00235%
38/1,613,986 alleles · very rare
exomes 33/1,461,836 · genomes 5/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00833% | 11,999 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| European (non-Finnish) | 0.00246% | 40,691 |
| South Asian | 0.0022% | 45,541 |
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.Pro337=
- Coding
- c.1011G>A
- MANE Select
- NM_024928
- dbSNP
- rs756692794
- Type
- single nucleotide variant
- Location
- chr10:103882780 (GRCh38)
- Gene constraint
- LOEUF 0.975 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.67 · 8 PDB
- Residue 337
- the 'winged helix-turn-helix (whth) 2' region
Similar variants
- STN1 p.Pro337Arg Uncertain significance ★ ⚠ same residue
- STN1 p.Pro337Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro337 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown