Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 48.5%, eas) — too common for a highly-penetrant pathogenic allele
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 -1.3 | GERP -3.8 |
| Overall | ||
| CADD | 0.759 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
48.5%
East Asian · 21,605/44,570 alleles
Filtering AF
47.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 47.7%
Overall
27.7%
444,739/1,607,748 alleles · common
exomes 394,682/1,455,844 · genomes 50,057/151,904 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 48.5% | 2 |
| African / African-American | 47.5% | 2 |
| Amishnot grpmax-eligible | 37.7% | 3 |
| South Asian | 31.6% | 3 |
| Admixed American | 29.4% | 3 |
| Remaining individualsnot grpmax-eligible | 28.3% | 4 |
| Middle Eastern | 27.6% | 4 |
| European (non-Finnish) | 25.6% | 4 |
| Finnishnot grpmax-eligible | 23.1% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 20% | 5 |
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.Ser918=
- Coding
- c.2754G>A
- MANE Select
- NM_001378778
- dbSNP
- rs2274856
- Type
- single nucleotide variant
- Location
- chr9:13176313 (GRCh38)
- Structure
- AlphaFold pLDDT 72.11 · 3 PDB
Similar variants
- MPDZ p.Ser918Leu Conflicting classifications of pathogenicity ★ ⚠ 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-ser918 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown