MPDZ p.Pro1382=
c.4146A>C · rs762053312 · VCV1647735
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00559%, nfe)
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 0.23 | GERP -3.5, phastCons 0.99 |
| Overall | ||
| CADD | 4.984 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00559%
European (non-Finnish) · 66/1,179,830 alleles
Filtering AF
0.00451%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00411%
Overall
0.00421%
68/1,613,786 alleles · very rare
exomes 54/1,461,602 · genomes 14/152,184 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00559% | 17,876 |
| Admixed American | 0.00167% | 60,004 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,462 |
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.Pro1382=
- Coding
- c.4146A>C
- MANE Select
- NM_001378778
- dbSNP
- rs762053312
- Type
- single nucleotide variant
- Location
- chr9:13138011 (GRCh38)
- Structure
- AlphaFold pLDDT 72.11 · 3 PDB
Similar variants
- MPDZ p.Pro1382Leu 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
- MPDZ p.Arg1071Ter 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-pro1382 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown