MST1 p.Arg535Pro
c.1604G>C · VCV3913892
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.718 | pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.43 | GERP -1.1, phastCons 0.093 |
| Overall | ||
| CADD | 25.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
African / African-American · 10/74,730 alleles
Filtering AF
0.00725%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00551%
Overall
0.000683%
11/1,609,532 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0134% | 7,473 |
| Admixed American | 0.00167% | 59,782 |
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.Arg535Pro
- Coding
- c.1604G>C
- MANE Select
- NM_006282 · reported on NM_020998
- Type
- single nucleotide variant
- Location
- chr3:49685030 (GRCh38)
- Structure
- AlphaFold pLDDT 76.45 · 16 PDB
Similar variants
- MST1 p.Arg535Gln Uncertain significance ★ same residue
- MST1 p.Arg535Trp 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
- STK4 p.Ala479Ser 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-arg535pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown