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MPDU1 mannose-P-dolichol utilization defect 1 [ Homo sapiens (human) ]

Gene ID: 9526, updated on 3-Apr-2024

Summary

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Official Symbol
MPDU1provided by HGNC
Official Full Name
mannose-P-dolichol utilization defect 1provided by HGNC
Primary source
HGNC:HGNC:7207
See related
Ensembl:ENSG00000129255 MIM:604041; AllianceGenome:HGNC:7207
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SL15; CDGIF; Lec35; My008; PQLC5; PP3958; SLC66A5; HBEBP2BPA
Summary
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]
Expression
Ubiquitous expression in colon (RPKM 20.5), duodenum (RPKM 20.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
17p13.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (7583647..7588212)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (7487897..7492462)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (7486965..7491530)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene SENP3-EIF4A1 readthrough (NMD candidate) Neighboring gene eukaryotic translation initiation factor 4A1 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:7481957-7482145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11634 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11635 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7485994-7486867 Neighboring gene small nucleolar RNA, H/ACA box 67 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7486868-7487742 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7487743-7488615 Neighboring gene MPDU1 antisense RNA 1 Neighboring gene CD68 molecule Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7492556-7493130 Neighboring gene SRY-box transcription factor 15 Neighboring gene FMR1 autosomal homolog 2 Neighboring gene uncharacterized LOC124904134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8133 Neighboring gene MPRA-validated peak2713 silencer Neighboring gene tRNA-undetermined (NNN) 6-1 Neighboring gene sex hormone binding globulin

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A mutation in the human MPDU1 gene causes congenital disorder of glycosylation type If (CDG-If). Kranz C, et al. J Clin Invest, 2001 Dec. PMID 11733556, Free PMC Article
  2. MPDU1 regulates CEACAM1 and cell adhesion in vitro and in vivo. Bennett DC, et al. Glycoconj J, 2018 Jun. PMID 29671116, Free PMC Article
  3. Expression cloning of a novel suppressor of the Lec15 and Lec35 glycosylation mutations of Chinese hamster ovary cells. Ware FE, et al. J Biol Chem, 1996 Jun 14. PMID 8663248
  4. MPDU1 mutations underlie a novel human congenital disorder of glycosylation, designated type If. Schenk B, et al. J Clin Invest, 2001 Dec. PMID 11733564, Free PMC Article
  5. Single-center experience of N-linked Congenital Disorders of Glycosylation with a Summary of Molecularly Characterized Cases in Arabs. Bastaki F, et al. Ann Hum Genet, 2018 Jan. PMID 28940310

See all (49) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. These experiments also confirmed that protein levels of CEACAM-1, which functions in cell adhesion, is dependent on LLO biosynthesis in vivo. Kato III cells and the MPDU1-rescued Kato IIIM cells therefore provide a novel model to examine the consequences of defective LLO biosynthesis both in vitro and in vivo.
    Title: MPDU1 regulates CEACAM1 and cell adhesion in vitro and in vivo.
  2. Cystinosin, MPDU1, SWEETs and KDELR belong to a well-defined protein family with putative function of cargo receptors.
    Title: Cystinosin, MPDU1, SWEETs and KDELR belong to a well-defined protein family with putative function of cargo receptors involved in vesicle trafficking.
  3. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Polymorphisms in innate immunity genes and lung cancer risk in Xuanwei, China.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic susceptibility to distinct bladder cancer subphenotypes.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
MPDU1-congenital disorder of glycosylation
MedGen: C1836669 OMIM: 609180 GeneReviews: Not available
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EBI GWAS Catalog

Description
A genome-wide association study in Han Chinese identifies multiple susceptibility loci for IgA nephropathy.
EBI GWAS Catalog
Genome-wide association study of sex hormones, gonadotropins and sex hormone-binding protein in Chinese men.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ14836

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in dolichol-linked oligosaccharide biosynthetic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in oligosaccharide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in oligosaccharide biosynthetic process IDA
Inferred from Direct Assay
more info
  
involved_in oligosaccharide biosynthetic process IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in protein folding NAS
Non-traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane NAS
Non-traceable Author Statement
more info
  
located_in membrane HDA PubMed 

General protein information

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Preferred Names
mannose-P-dolichol utilization defect 1 protein
Names
HBeAg-binding protein 2 binding protein A
suppressor of Lec15 and Lec35 glycosylation mutation homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009204.1 RefSeqGene

    Range
    5206..9566
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001330073.1 → NP_001317002.1  mannose-P-dolichol utilization defect 1 protein isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site and lacks an alternate exon in the 3' coding region, resulting in a frameshift and an early stop codon compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC016876, AF038961, BQ002417, BX422669, DC421138
    Consensus CDS
    CCDS82054.1
    UniProtKB/TrEMBL
    J3QW43
    Related
    ENSP00000379758.4, ENST00000396501.8
    Conserved Domains (1) summary
    TIGR00951
    Location:40 → 130
    2A43; Lysosomal Cystine Transporter

  2. NM_004870.4 → NP_004861.2  mannose-P-dolichol utilization defect 1 protein isoform 1

    See identical proteins and their annotated locations for NP_004861.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC001898, BG776573, BM127836, BQ002417
    Consensus CDS
    CCDS11115.1
    UniProtKB/Swiss-Prot
    B3KQP1, B4DT74, O75352, Q9BUU8
    UniProtKB/TrEMBL
    A0A0S2Z4W8, A0A291FGC8, A0A291FGE0, B2RB74
    Related
    ENSP00000250124.6, ENST00000250124.11
    Conserved Domains (1) summary
    TIGR00951
    Location:40 → 235
    2A43; Lysosomal Cystine Transporter

RNA

  1. NR_024603.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region that causes a frameshift and early stop codon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK300140, BG776573, BM127836, BQ002417, DC421138

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    7583647..7588212
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006721598.4 → XP_006721661.1  mannose-P-dolichol utilization defect 1 protein isoform X2

    See identical proteins and their annotated locations for XP_006721661.1

    UniProtKB/TrEMBL
    B4DLH7, E7ERF8, Q9H3L2
    Related
    ENST00000572836.5
    Conserved Domains (2) summary
    TIGR00951
    Location:40 → 168
    2A43; Lysosomal Cystine Transporter
    pfam04193
    Location:43 → 101
    PQ-loop; PQ loop repeat

  2. XM_006721597.3 → XP_006721660.1  mannose-P-dolichol utilization defect 1 protein isoform X1

    See identical proteins and their annotated locations for XP_006721660.1

    UniProtKB/TrEMBL
    E7ES02, Q1HDL3
    Conserved Domains (1) summary
    pfam04193
    Location:43 → 101
    PQ-loop; PQ loop repeat

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    7487897..7492462
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054317878.1 → XP_054173853.1  mannose-P-dolichol utilization defect 1 protein isoform X2

    UniProtKB/TrEMBL
    B4DLH7

  2. XM_054317877.1 → XP_054173852.1  mannose-P-dolichol utilization defect 1 protein isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75352.2 GenPept UniProtKB/Swiss-Prot:O75352

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