Is MPDZ p.Arg9Trp (c.25C>T) pathogenic?

MPDZ p.Arg9Trp (c.25C>T) is classified Uncertain significance in MPDZ (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-08-29). AlphaMissense: likely benign (0.3056); Ultra-rare (popmax 0.0332%, mid); Associated with Inborn genetic diseases.

What condition is associated with MPDZ p.Arg9Trp (c.25C>T)?

MPDZ p.Arg9Trp (c.25C>T) is associated with Inborn genetic diseases (ClinVar).

How common is MPDZ p.Arg9Trp (c.25C>T) in the general population?

MPDZ p.Arg9Trp (c.25C>T) is ultra-rare (popmax 0.0332%, mid) (gnomAD).

What do computational predictors say about MPDZ p.Arg9Trp (c.25C>T)?

AlphaMissense predicts likely benign (score 0.3056) — an in-silico prediction, not a clinical call.

MPDZ p.Arg9Trp

c.25C>T · rs777301563 · VCV1439211

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.3056 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0332%, mid)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3056	likely benign
REVEL	0.446	indeterminate
SaProt	LLR -10.67	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.6	GERP 2.3, phastCons 1
Overall
CADD	26.2	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 0.0332% Middle Eastern · 2/6,020 alleles

Filtering AF 0.00585% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00269%

Overall 0.00412% 66/1,602,026 alleles · ultra-rare exomes 61/1,449,868 · genomes 5/152,158 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0332%	3,010
South Asian	0.00775%	12,908
Admixed American	0.00669%	14,956
Remaining individualsnot grpmax-eligible	0.00647%	15,466
African / African-American	0.00401%	24,919
European (non-Finnish)	0.00393%	25,449

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.Arg9Trp
Coding: c.25C>T
MANE Select: NM_001378778
dbSNP: rs777301563
Type: single nucleotide variant
Location: chr9:13247793 (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-arg9trp (accessed [today's date]).

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