Is MPDU1 p.Val131= (c.393C>T) pathogenic?

MPDU1 p.Val131= (c.393C>T) is classified Conflicting classifications of pathogenicity in MPDU1 (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-01-14). Rare (popmax 0.333%, afr); Associated with MPDU1-congenital disorder of glycosylation.

What condition is associated with MPDU1 p.Val131= (c.393C>T)?

MPDU1 p.Val131= (c.393C>T) is associated with MPDU1-congenital disorder of glycosylation (ClinVar).

How common is MPDU1 p.Val131= (c.393C>T) in the general population?

MPDU1 p.Val131= (c.393C>T) is rare (popmax 0.333%, afr) (gnomAD).

How is MPDU1-CDG inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

MPDU1 p.Val131=

c.393C>T · rs79286384 · VCV325515

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.333%, afr)

Conditions

MPDU1-congenital disorder of glycosylation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.265	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5	GERP -4.8
Overall
CADD	11.11	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.333% African / African-American · 250/74,982 alleles

Filtering AF 0.299% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.286%

Overall 0.122% 1,977/1,613,996 alleles · rare exomes 1,719/1,461,806 · genomes 258/152,190 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.333%	300
Remaining individualsnot grpmax-eligible	0.163%	613
Admixed American	0.162%	619
European (non-Finnish)	0.126%	794
South Asian	0.0417%	2,397
Middle Eastern	0.0165%	6,062
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,606
East Asian	0.00223%	44,874

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: MPDU1
Protein: p.Val131=
Coding: c.393C>T
MANE Select: NM_004870
dbSNP: rs79286384
Type: single nucleotide variant
Location: chr17:7586903 (GRCh38)
Gene constraint: LOEUF 0.984 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.57

Full MPDU1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MPDU1-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For MPDU1-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

MPDU1 p.Ala187Val Uncertain significance ★★ ⚠ same condition
MPDU1 p.Arg200Gln Uncertain significance ★★ ⚠ same condition
MPDU1 p.Ile50Thr Uncertain significance ★★ ⚠ same condition
MPDU1 p.Lys238Arg Uncertain significance ★★ ⚠ same condition
MPDU1 p.Thr113Met Uncertain significance ★★ ⚠ same condition
MPDU1 c.103+19C>T Likely benign ★★ same condition
MPDU1 c.169+14C>T Likely benign ★★ same condition
MPDU1 c.619-17C>G Likely benign ★★ 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/mpdu1-p-val131 (accessed [today's date]).

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