MAST1 p.Pro698=
c.2094C>T · rs148936558 · VCV2172747
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.1 | GERP -3.7 |
| Overall | ||
| CADD | 7.232 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,082 alleles
Filtering AF
0.00394%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00361%
Overall
0.00508%
82/1,613,806 alleles · ultra-rare
exomes 69/1,461,652 · genomes 13/152,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,082 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,809 |
| Finnishnot grpmax-eligible | 0.00782% | 12,790 |
| Admixed American | 0.00667% | 14,993 |
| European (non-Finnish) | 0.005% | 19,999 |
| South Asian | 0.00439% | 22,766 |
| African / African-American | 0.00133% | 74,914 |
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
- MAST1
- Protein
- p.Pro698=
- Coding
- c.2094C>T
- MANE Select
- NM_014975
- dbSNP
- rs148936558
- Type
- single nucleotide variant
- Location
- chr19:12866717 (GRCh38)
- Gene constraint
- LOEUF 0.379 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.19 · 2 PDB
- Residue 698
- the agc-kinase c-terminal domain
Similar variants
- MAST1 p.Pro698Thr Uncertain significance ★★ ⚠ same residue
- MAST1 p.Gly517Ser Pathogenic ★★ same type
- MAST1 p.Pro1177Leu Likely pathogenic ★★ ⚠ same type
- MAST1 c.3263+5G>A Uncertain significance ★★ same type
- MAST1 p.Ala1410Thr Uncertain significance ★★ ⚠ same type
- MAST1 p.Ala1455Val Uncertain significance ★★ ⚠ same type
- MAST1 p.Ala887Val Uncertain significance ★★ ⚠ same type
- MAST1 p.Arg1422Gln 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/mast1-p-pro698 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown