MBTPS2 p.Pro428=
c.1284A>G · rs2092958634 · VCV1546941
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00174%, 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 4.5 | GERP -0.34, phastCons 1 |
| Overall | ||
| CADD | 10.64 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00174%
African / African-American · 1/57,548 alleles
Overall
8.32e-05%
1/1,201,493 alleles · very rare
exomes 1/1,088,118 · genomes 0/113,375 · joint denominator
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
- MBTPS2
- Protein
- p.Pro428=
- Coding
- c.1284A>G
- MANE Select
- NM_015884
- dbSNP
- rs2092958634
- Type
- single nucleotide variant
- Location
- chrX:21880919 (GRCh38)
- Structure
- AlphaFold pLDDT 87.78
Similar variants
- MBTPS2 c.970+5G>A Pathogenic ★★ same type
- MBTPS2 p.Arg429His Pathogenic ★★ same type
- MBTPS2 p.Asn508Ser Pathogenic ★★ same type
- MBTPS2 p.Ala507Val Uncertain significance ★★ same type
- MBTPS2 p.Arg327Gln Uncertain significance ★★ ⚠ same type
- MBTPS2 p.Arg59His Uncertain significance ★★ ⚠ same type
- MBTPS2 p.Asn40Thr Uncertain significance ★★ ⚠ same type
- MBTPS2 p.Asp292Gly 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/mbtps2-p-pro428 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown