MPDU1

Chr 17AR

mannose-P-dolichol utilization defect 1

Also known as: CDGIF, HBEBP2BPA, Lec35, My008, PP3958, PQLC5, SL15, SLC66A5

NCBI Gene: 9526 ENSG00000129255 UniProt: O75352 OMIM: 604041

The encoded endoplasmic reticulum membrane protein is required for normal utilization of mannose-dolichol phosphate in the synthesis of N-linked and O-linked oligosaccharides and GPI anchors. Mutations cause congenital disorder of glycosylation type If, which follows autosomal recessive inheritance. The gene shows low constraint to loss-of-function variation (pLI <0.001, LOEUF 1.31).

OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes an endoplasmic reticulum membrane protein that is required for utilization of the mannose donor mannose-P-dolichol in the synthesis of lipid-linked oligosaccharides and glycosylphosphatidylinositols. Mutations in this gene result in congenital disorder of glycosylation type If. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2008]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Congenital disorder of glycosylation, type IfMIM #609180

Clinical highlights

Gene–disease validity (ClinGen)

Definitive · MPDU1-congenital disorder of glycosylation · AR · ClinGen 2025

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

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P/LP missense

—

LOEUF

LOF

Mechanism· G2P

Some data sources returned errors (1)

gnomad: Error: gnomAD API error: 400

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in MPDU1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 120

421 rare PASS variants

Rare truncating (LoF)

1 in 1,800

78 rare PASS variants

Rare synonymous (reference)

1 in 790

118 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for MPDU1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 160	1 in 1,900
South Asian	~43k	1 in 170	1 in 1,200
Remaining (unassigned)	~30k	1 in 140	1 in 3,800
European (Finnish)	~27k	1 in 310	≈ 1 in 7,900
Admixed American	~22k	1 in 190	1 in 1,000
African / African American	~21k	1 in 110	1 in 400
East Asian	~20k	1 in 230	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 520	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 160	≈ 1 in 1,400

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 7 of 7 coding exons well covered in gnomAD exomes. Genomes: 6 of 7 (exon 5 below).? see exons ↓