Is MPDZ p.Cys810Ser (c.2429G>C) pathogenic?

MPDZ p.Cys810Ser (c.2429G>C) is classified Benign/Likely benign in MPDZ (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-09). AlphaMissense: likely benign (0.08); Rare (popmax 0.308%, eas); Associated with Inborn genetic diseases.

What condition is associated with MPDZ p.Cys810Ser (c.2429G>C)?

MPDZ p.Cys810Ser (c.2429G>C) is associated with Inborn genetic diseases (ClinVar).

How common is MPDZ p.Cys810Ser (c.2429G>C) in the general population?

MPDZ p.Cys810Ser (c.2429G>C) is rare (popmax 0.308%, eas) (gnomAD).

What do computational predictors say about MPDZ p.Cys810Ser (c.2429G>C)?

AlphaMissense predicts likely benign (score 0.08) — an in-silico prediction, not a clinical call.

MPDZ p.Cys810Ser

c.2429G>C · rs200535644 · VCV727615

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.08 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.308%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.08	likely benign
REVEL	0.038	moderately benign-leaning
SaProt	LLR -3.56	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP 0.58, phastCons 0.8
Overall
CADD	13.41	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.308% East Asian · 136/44,144 alleles

Filtering AF 0.266% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.25%

Overall 0.0109% 174/1,596,898 alleles · rare exomes 148/1,444,746 · genomes 26/152,152 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.308%	325
Remaining individualsnot grpmax-eligible	0.0485%	2,062
South Asian	0.00569%	17,560
European (non-Finnish)	0.000256%	390,411

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.Cys810Ser
Coding: c.2429G>C
MANE Select: NM_001378778
dbSNP: rs200535644
Type: single nucleotide variant
Location: chr9:13186322 (GRCh38)
Structure: AlphaFold pLDDT 72.11 · 3 PDB

Full MPDZ gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MPDZ p.Arg449Ter Pathogenic/Likely pathogenic ★★ same condition
MPDZ c.3254+6T>C Uncertain significance ★★ same condition
MPDZ c.5558-3C>T Uncertain significance ★★ same condition
MPDZ p.Ala104Thr Uncertain significance ★★ ⚠ same condition
MPDZ p.Ala1068Asp Uncertain significance ★★ ⚠ same condition
MPDZ p.Ala10Val Uncertain significance ★★ ⚠ same condition
MPDZ p.Ala1196Gly Uncertain significance ★★ ⚠ same condition
MPDZ p.Ala1227Thr Uncertain significance ★★ ⚠ same condition

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-cys810ser (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown