MPDZ p.Pro1598=
c.4794G>A · VCV3389355
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00447%, 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 -9.2 | GERP -4.5 |
| Overall | ||
| CADD | 0.945 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00447%
South Asian · 4/89,524 alleles
Filtering AF
0.00144%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000903%
Overall
0.000688%
11/1,598,746 alleles · very rare
exomes 9/1,446,700 · genomes 2/152,046 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00447% | 22,381 |
| East Asian | 0.00224% | 44,656 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,660 |
| European (non-Finnish) | 0.000427% | 234,076 |
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.Pro1598=
- Coding
- c.4794G>A
- MANE Select
- NM_001378778
- Type
- single nucleotide variant
- Location
- chr9:13125229 (GRCh38)
- Structure
- AlphaFold pLDDT 72.11 · 3 PDB
Similar variants
- 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
- MPDZ p.Arg1071Ter Pathogenic ★★ same type
- MPDZ p.Arg1170Ter 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-pro1598 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown