MAST3 p.Pro747=
c.2241C>T · VCV3905627
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00193%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP 1.4 |
| Overall | ||
| CADD | 7.957 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00193%
European (non-Finnish) · 22/1,140,664 alleles
Filtering AF
0.00126%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00108%
Overall
0.00149%
23/1,539,122 alleles · very rare
exomes 21/1,387,044 · genomes 2/152,078 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00193% | 51,848 |
| Remaining individualsnot grpmax-eligible | 0.00169% | 59,202 |
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.Pro747=
- Coding
- c.2241C>T
- MANE Select
- NM_001393504
- Type
- single nucleotide variant
- Location
- chr19:18141917 (GRCh38)
- Gene constraint
- LOEUF 0.466 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 58.00 · 2 PDB
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-pro747 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown