MST1 p.Pro19Ser
c.55C>T · rs62262686 · VCV156207
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 24.3%, amr) — 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. | ||
| REVEL | 0.183 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -2.6, phastCons 1 |
| Overall | ||
| CADD | 17.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
24.3%
Admixed American · 7,518/30,936 alleles
Filtering AF
23.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 23.7%
Overall
15.8%
121,657/768,512 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 24.3% | 4 |
| Finnishnot grpmax-eligible | 23.1% | 4 |
| South Asian | 22.8% | 4 |
| Middle Eastern | 21.2% | 5 |
| African / African-American | 18.8% | 5 |
| East Asian | 17.2% | 6 |
| Remaining individualsnot grpmax-eligible | 14.8% | 7 |
| European (non-Finnish) | 14.2% | 7 |
| Ashkenazi Jewishnot grpmax-eligible | 12.9% | 8 |
| Amishnot grpmax-eligible | 7.87% | 13 |
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.Pro19Ser
- Coding
- c.55C>T
- MANE Select
- NM_006282 · reported on NM_020998
- dbSNP
- rs62262686
- Type
- single nucleotide variant
- Location
- chr3:49688637 (GRCh38)
- Structure
- AlphaFold pLDDT 76.45 · 16 PDB
- Residue 19
- an α-helix
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-pro19ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown