MAST3 p.Pro971=
c.2913C>T · VCV4941552
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.196%, afr)
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 -20 | GERP -3.7 |
| Overall | ||
| CADD | 1.966 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.196%
African / African-American · 147/75,020 alleles
Filtering AF
0.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.16%
Overall
0.0212%
342/1,613,782 alleles · rare
exomes 234/1,461,520 · genomes 108/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.196% | 510 |
| Ashkenazi Jewishnot grpmax-eligible | 0.193% | 519 |
| Middle Eastern | 0.148% | 674 |
| Admixed American | 0.035% | 2,858 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,289 |
| European (non-Finnish) | 0.00729% | 13,719 |
| South Asian | 0.00329% | 30,359 |
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
- MAST3
- Protein
- p.Pro971=
- Coding
- c.2913C>T
- MANE Select
- NM_001393504
- Type
- single nucleotide variant
- Location
- chr19:18145103 (GRCh38)
- Gene constraint
- LOEUF 0.466 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 58.00 · 2 PDB
- Residue 971
- the pdz domain; a β-strand
Similar variants
- MAST3 p.Gly539Ser Pathogenic/Likely pathogenic ★★ same type
- MAST3 p.Gly544Ser Pathogenic ★★ ⚠ same type
- MAST3 p.Arg780Trp Uncertain significance ★★ ⚠ same type
- MAST3 p.Glu1285Lys Uncertain significance ★★ same type
- MAST3 p.Glu1334Lys Uncertain significance ★★ ⚠ same type
- MAST3 p.Glu368Lys Uncertain significance ★★ ⚠ same type
- MAST3 p.Glu579Lys Uncertain significance ★★ ⚠ same type
- MAST3 p.Glu713Lys 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/mast3-p-pro971 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown