MPDZ p.Pro788=
c.2364C>T · rs769078887 · VCV1303774
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0265%, sas)
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 -2.8 | GERP -4.7 |
| Overall | ||
| CADD | 0.244 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0265%
South Asian · 24/90,562 alleles
Filtering AF
0.0182%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0155%
Overall
0.00385%
62/1,609,004 alleles · ultra-rare
exomes 58/1,456,922 · genomes 4/152,082 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0265% | 3,773 |
| Remaining individualsnot grpmax-eligible | 0.0209% | 4,789 |
| African / African-American | 0.00803% | 12,452 |
| East Asian | 0.00223% | 44,746 |
| Admixed American | 0.00167% | 59,710 |
| European (non-Finnish) | 0.00144% | 69,219 |
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
- MPDZ
- Protein
- p.Pro788=
- Coding
- c.2364C>T
- MANE Select
- NM_001378778
- dbSNP
- rs769078887
- Type
- single nucleotide variant
- Location
- chr9:13188784 (GRCh38)
- Structure
- AlphaFold pLDDT 72.11 · 3 PDB
Similar variants
- MPDZ p.Pro788Thr Benign/Likely benign ★★ same residue
- MPDZ p.Pro788Ser Uncertain significance ★ ⚠ same residue
- MPDZ c.1087-1G>A Pathogenic/Likely pathogenic ★★ same type
- MPDZ c.1474+2T>C Likely pathogenic ★★ same type
- MPDZ c.3359+1G>A Likely pathogenic ★★ same type
- MPDZ c.3360-2A>G Pathogenic/Likely pathogenic ★★ same type
- MPDZ c.4003+1G>A Pathogenic/Likely pathogenic ★★ same type
- MPDZ p.Arg1034Ter Pathogenic/Likely pathogenic ★★ 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/mpdz-p-pro788 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown