Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 94%, eas) — too common for a highly-penetrant pathogenic allele
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 -9.2 | GERP -5.2 |
| Overall | ||
| CADD | 3.874 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
94%
East Asian · 40,784/43,406 alleles
Filtering AF
93.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 92.9%
Overall
51%
776,663/1,521,396 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 94% | 1 |
| South Asian | 66.4% | 2 |
| Admixed American | 65.5% | 2 |
| Amishnot grpmax-eligible | 59.2% | 2 |
| Remaining individualsnot grpmax-eligible | 51.7% | 2 |
| European (non-Finnish) | 48.8% | 2 |
| Finnishnot grpmax-eligible | 48.7% | 2 |
| Middle Eastern | 46.7% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 42.5% | 2 |
| African / African-American | 34.7% | 3 |
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
- MST1
- Protein
- p.Pro326=
- Coding
- c.978G>T
- MANE Select
- NM_006282 · reported on NM_020998
- dbSNP
- rs9713651
- Type
- single nucleotide variant
- Location
- chr3:49686351 (GRCh38)
- Structure
- AlphaFold pLDDT 76.45 · 16 PDB
- Residue 326
- a functional site (cleavage; by caspase-3); the 'disordered' region
Similar variants
- STK4 p.Arg115Ter Pathogenic/Likely pathogenic ★★ same type
- STK4 p.Arg117Ter Pathogenic ★★ same type
- STK4 p.Arg148Ter Pathogenic ★★ same type
- STK4 p.Arg245Ter Pathogenic/Likely pathogenic ★★ same type
- STK4 p.Ala391Val Uncertain significance ★★ ⚠ same type
- STK4 p.Ala479Ser Uncertain significance ★★ ⚠ same type
- STK4 p.Arg310Gln Uncertain significance ★★ ⚠ same type
- STK4 p.Arg310Pro 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/mst1-p-pro326 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown