MST1 p.Ser702Pro
c.2104T>C · VCV3399071
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.263 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.5 | GERP -0.96, phastCons 1 |
| Regional constraint | o/e 0.88 | unconstrained · MANE · 3,797 bp · p 0.00036 · regional, not allelic |
| Overall | ||
| CADD | 14.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,898 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,613,506 alleles · very rare
exomes 2/1,461,338 · genomes 1/152,168 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,898 |
| European (non-Finnish) | 0.00017% | 589,936 |
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.Ser702Pro
- Coding
- c.2104T>C
- MANE Select
- NM_020998
- Type
- single nucleotide variant
- Location
- chr3:49684102 (GRCh38)
- Gene constraint
- LOEUF 0.951 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.30 · 2 PDB
- Residue 702
- an α-helix; the peptidase s1 domain
Similar variants
- MST1 p.Ser702= Likely benign ★ 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-ser702pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown