Is MPDU1 p.Val28= (c.84T>C) pathogenic?

MPDU1 p.Val28= (c.84T>C) is classified Uncertain significance in MPDU1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-12). Very rare (popmax 8.47e-05%, nfe); Associated with MPDU1-congenital disorder of glycosylation.

What condition is associated with MPDU1 p.Val28= (c.84T>C)?

MPDU1 p.Val28= (c.84T>C) is associated with MPDU1-congenital disorder of glycosylation (ClinVar).

How common is MPDU1 p.Val28= (c.84T>C) in the general population?

MPDU1 p.Val28= (c.84T>C) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

How is MPDU1-CDG inherited?

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

MPDU1 p.Val28=

c.84T>C · rs1430454810 · VCV889662

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

MPDU1-congenital disorder of glycosylation

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 -0.44	GERP -2, phastCons 0.053
Overall
CADD	16.12	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,048 alleles

Overall 6.2e-05% 1/1,614,044 alleles · very rare exomes 0/1,461,784 · genomes 1/152,260 · joint denominator

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.Val28=
Coding: c.84T>C
MANE Select: NM_004870
dbSNP: rs1430454810
Type: single nucleotide variant
Location: chr17:7583946 (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.Val28Ile Uncertain significance ★ ⚠ same residue
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

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-val28 (accessed [today's date]).

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