MST1 p.Ser101Pro
c.301T>C · rs1292497022 · VCV2482798
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.463 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 9.2 | GERP 2.4, phastCons 1 |
| Regional constraint | o/e 0.88 | unconstrained · MANE · 3,797 bp · p 0.00036 · regional, not allelic |
| Overall | ||
| CADD | 24.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,070 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000434%
7/1,613,320 alleles · very rare
exomes 5/1,461,252 · genomes 2/152,068 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,070 |
| European (non-Finnish) | 0.000509% | 196,641 |
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.Ser101Pro
- Coding
- c.301T>C
- MANE Select
- NM_020998
- dbSNP
- rs1292497022
- Type
- single nucleotide variant
- Location
- chr3:49687610 (GRCh38)
- Gene constraint
- LOEUF 0.951 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.30 · 2 PDB
- Residue 101
- the pan domain
Similar variants
- MST1 p.Ser101Leu Uncertain significance ★ same residue
- MST1 p.Gly215Arg Benign ★★ same type
- MST1 p.Pro326= Likely benign ★★ same type
- MST1 p.Ser511= Benign/Likely benign ★★ same type
- MST1 p.Thr313= Likely benign ★★ same type
- MST1 p.Ala323Thr Uncertain significance ★ same type
- MST1 p.Ala410Thr Uncertain significance ★ same type
- MST1 p.Ala54Val 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-ser101pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown