MAST4 p.Pro130=
c.390C>T · rs565434858 · VCV713220
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.51%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.164 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.22 | GERP 2.4, phastCons 0.22 |
| Overall | ||
| CADD | 8.341 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.51%
East Asian · 229/44,888 alleles
Filtering AF
0.456%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.435%
Overall
0.0149%
241/1,613,982 alleles · rare
exomes 213/1,461,664 · genomes 28/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.51% | 196 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,810 |
| South Asian | 0.0011% | 91,070 |
| European (non-Finnish) | 0.00017% | 589,939 |
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
- MAST4
- Protein
- p.Pro130=
- Coding
- c.390C>T
- MANE Select
- NM_001164664
- dbSNP
- rs565434858
- Type
- single nucleotide variant
- Location
- chr5:66759735 (GRCh38)
- Gene constraint
- LOEUF 0.66 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 43.32 · 1 PDB
- Residue 130
- the 'disordered' region
Similar variants
- MAST4 p.Arg2128Ser Benign ★★ same type
- MAST4 p.Gln161= Benign ★★ same type
- MAST4 p.Leu681= Benign ★★ same type
- MAST4 p.Thr2354= Benign ★★ same type
- MAST4 c.3526-3T>C Uncertain significance ★ same type
- MAST4 c.642+40063G>C Uncertain significance ★ same type
- MAST4 c.642+40066T>C Uncertain significance ★ same type
- MAST4 c.642+40075G>A 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/mast4-p-pro130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown