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

    Gene ID: 9526, updated on 2-Nov-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
    mouse all
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    Genomic context

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    See MPDU1 in Genome Data Viewer
    Location:
    17p13.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (7583647..7588212)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (7487897..7492462)
    RS_2024_09 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 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. 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
    3. MPDU1 regulates CEACAM1 and cell adhesion in vitro and in vivo. Bennett DC, et al. Glycoconj J, 2018 Jun. PMID 29671116, Free PMC Article
    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. Cystinosin, MPDU1, SWEETs and KDELR belong to a well-defined protein family with putative function of cargo receptors involved in vesicle trafficking. Saudek V. PLoS One, 2012. PMID 22363504, Free PMC Article

    See all (54) 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
    		Compare labs

    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_2024_08

    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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