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DPM1 dolichyl-phosphate mannosyltransferase subunit 1, catalytic [ Homo sapiens (human) ]

Gene ID: 8813, updated on 14-Nov-2024

Summary

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Official Symbol
DPM1provided by HGNC
Official Full Name
dolichyl-phosphate mannosyltransferase subunit 1, catalyticprovided by HGNC
Primary source
HGNC:HGNC:3005
See related
Ensembl:ENSG00000000419 MIM:603503; AllianceGenome:HGNC:3005
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
MPDS; CDGIE
Summary
Dolichol-phosphate mannose (Dol-P-Man) serves as a donor of mannosyl residues on the lumenal side of the endoplasmic reticulum (ER). Lack of Dol-P-Man results in defective surface expression of GPI-anchored proteins. Dol-P-Man is synthesized from GDP-mannose and dolichol-phosphate on the cytosolic side of the ER by the enzyme dolichyl-phosphate mannosyltransferase. Human DPM1 lacks a carboxy-terminal transmembrane domain and signal sequence and is regulated by DPM2. Mutations in this gene are associated with congenital disorder of glycosylation type Ie. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2015]
Expression
Ubiquitous expression in adrenal (RPKM 24.6), thyroid (RPKM 23.5) and 25 other tissues See more
Orthologs
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Genomic context

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See DPM1 in Genome Data Viewer
Location:
20q13.13
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (50934855..50958564, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (52705454..52729167, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (49551392..49575101, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene breast carcinoma amplified sequence 4 Neighboring gene uncharacterized LOC124904929 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49486444-49487157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49487158-49487870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49488585-49489297 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49491439-49492150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49492678-49493258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49495917-49496418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49496419-49496918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13031 Neighboring gene activity dependent neuroprotector homeobox Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49541986-49542486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49542487-49542987 Neighboring gene proteasome 26S subunit, non-ATPase, 10 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13033 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13032 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:49546803-49547593 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13036 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18107 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:49548232-49548419 Neighboring gene ADNP antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49575528-49576138 Neighboring gene molybdenum cofactor synthesis 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49606180-49607142 Neighboring gene Sharpr-MPRA regulatory region 8647 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:49620535-49621036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:49637285-49637848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13038 Neighboring gene potassium voltage-gated channel modifier subfamily G member 1

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. Dolichol phosphate mannose synthase (DPM1) mutations define congenital disorder of glycosylation Ie (CDG-Ie). Kim S, et al. J Clin Invest, 2000 Jan. PMID 10642597, Free PMC Article
  2. Congenital disorder of glycosylation (CDG) type Ie. A new patient. García-Silva MT, et al. J Inherit Metab Dis, 2004. PMID 15669674
  3. Deficiency of dolichol-phosphate-mannose synthase-1 causes congenital disorder of glycosylation type Ie. Imbach T, et al. J Clin Invest, 2000 Jan. PMID 10642602, Free PMC Article
  4. Human and Saccharomyces cerevisiae dolichol phosphate mannose synthases represent two classes of the enzyme, but both function in Schizosaccharomyces pombe. Colussi PA, et al. Proc Natl Acad Sci U S A, 1997 Jul 22. PMID 9223280, Free PMC Article
  5. Congenital disorder of glycosylation due to DPM1 mutations presenting with dystroglycanopathy-type congenital muscular dystrophy. Yang AC, et al. Mol Genet Metab, 2013 Nov. PMID 23856421, Free PMC Article

See all (158) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DPM1 modulates desmosomal adhesion and epidermal differentiation through SERPINB5.
    Title: DPM1 modulates desmosomal adhesion and epidermal differentiation through SERPINB5.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Congenital disorder of glycosylation type 1E
MedGen: C1837396 OMIM: 608799 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit (DPM1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables D-mannose binding IEA
Inferred from Electronic Annotation
more info
  
enables alcohol binding IEA
Inferred from Electronic Annotation
more info
  
enables dolichyl-phosphate beta-D-mannosyltransferase activity EXP
Inferred from Experiment
more info
 PubMed 
enables dolichyl-phosphate beta-D-mannosyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables dolichyl-phosphate beta-D-mannosyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables dolichyl-phosphate-mannose-protein mannosyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in GDP-mannose metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in GPI anchor biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within GPI anchor biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in GPI anchor biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within dolichol metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in dolichol metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in dolichol phosphate mannose biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in dolichol-linked oligosaccharide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein N-linked glycosylation via asparagine TAS
Traceable Author Statement
more info
  
involved_in protein O-linked mannosylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein O-linked mannosylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein mannosylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to oxygen levels IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of dolichol-phosphate-mannose synthase complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of dolichol-phosphate-mannose synthase complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in membrane HDA PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus HDA PubMed 

General protein information

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Preferred Names
dolichol-phosphate mannosyltransferase subunit 1
Names
DPM synthase complex, catalytic subunit
DPM synthase subunit 1
MPD synthase subunit 1
dolichol monophosphate mannose synthase
dolichol-phosphate mannose synthase subunit 1
dolichyl-phosphate beta-D-mannosyltransferase subunit 1
dolichyl-phosphate mannosyltransferase polypeptide 1 catalytic subunit
mannose-P-dolichol synthase subunit 1
NP_001303963.1
NP_001303964.1
NP_001303965.1
NP_003850.1
XP_047296533.1
XP_054180171.1

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_008923.1 RefSeqGene

    Range
    4992..28654
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001317034.1 → NP_001303963.1  dolichol-phosphate mannosyltransferase subunit 1 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL034553, BC007073, CA865473, DR156925
    Consensus CDS
    CCDS93059.1
    UniProtKB/TrEMBL
    H0Y368
    Related
    ENSP00000360640.5, ENST00000371584.9
    Conserved Domains (3) summary
    cd06442
    Location:29 → 291
    DPM1_like; DPM1_like represents putative enzymes similar to eukaryotic DPM1
    PLN02726
    Location:23 → 295
    PLN02726; dolichyl-phosphate beta-D-mannosyltransferase
    pfam13900
    Location:175 → 206
    GVQW; Putative domain of unknown function

  2. NM_001317035.1 → NP_001303964.1  dolichol-phosphate mannosyltransferase subunit 1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AL034553, BC007073, BM922866, CA865473
    Consensus CDS
    CCDS82628.1
    UniProtKB/TrEMBL
    Q5QPK2
    Related
    ENSP00000360638.4, ENST00000371582.8
    Conserved Domains (2) summary
    cd06442
    Location:29 → 283
    DPM1_like; DPM1_like represents putative enzymes similar to eukaryotic DPM1
    PLN02726
    Location:23 → 287
    PLN02726; dolichyl-phosphate beta-D-mannosyltransferase

  3. NM_001317036.1 → NP_001303965.1  dolichol-phosphate mannosyltransferase subunit 1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two alternate in-frame exons in the 3' coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AL034553, BC007073, BQ441542, CA865473
    UniProtKB/Swiss-Prot
    O60762
    Conserved Domains (2) summary
    cd06442
    Location:29 → 233
    DPM1_like; DPM1_like represents putative enzymes similar to eukaryotic DPM1
    PLN02726
    Location:23 → 237
    PLN02726; dolichyl-phosphate beta-D-mannosyltransferase

  4. NM_003859.3 → NP_003850.1  dolichol-phosphate mannosyltransferase subunit 1 isoform 3

    See identical proteins and their annotated locations for NP_003850.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    BC016322, D86198
    Consensus CDS
    CCDS13434.1
    UniProtKB/Swiss-Prot
    O15157, O60762, Q6IB78, Q96HK0
    UniProtKB/TrEMBL
    A0A0S2Z4Y5, Q5QPJ9
    Related
    ENSP00000360644.5, ENST00000371588.10
    Conserved Domains (1) summary
    PLN02726
    Location:23 → 260
    PLN02726; dolichyl-phosphate beta-D-mannosyltransferase

RNA

  1. NR_133648.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate internal exon, and uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL034553, BC008427
    Related
    ENST00000466152.5

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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    50934855..50958564 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047440577.1 → XP_047296533.1  dolichol-phosphate mannosyltransferase subunit 1 isoform X1

RNA

  1. XR_007067482.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    52705454..52729167 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324196.1 → XP_054180171.1  dolichol-phosphate mannosyltransferase subunit 1 isoform X1

RNA

  1. XR_008485315.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60762.1 GenPept UniProtKB/Swiss-Prot:O60762

Gene LinkOut

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