MST1 p.Arg434Pro
c.1301G>C · VCV4553595
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0214%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.908 | moderately pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 2.8, phastCons 1 |
| Overall | ||
| CADD | 28.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0214%
African / African-American · 16/74,928 alleles
Filtering AF
0.0133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0109%
Overall
0.00105%
17/1,613,304 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0214% | 4,683 |
| South Asian | 0.0011% | 91,082 |
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.Arg434Pro
- Coding
- c.1301G>C
- MANE Select
- NM_006282 · reported on NM_020998
- Type
- single nucleotide variant
- Location
- chr3:49685682 (GRCh38)
- Structure
- AlphaFold pLDDT 76.45 · 16 PDB
- Residue 434
- the sarah domain; an α-helix
Similar variants
- STK4 p.Glu434Lys Uncertain significance ★★ ⚠ same residue
- MST1 p.Arg434Gln Uncertain significance ★ same residue
- MST1 p.Arg434Trp Uncertain significance ★ same residue
- 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
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-arg434pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown