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DPM3 dolichyl-phosphate mannosyltransferase subunit 3, regulatory [ Homo sapiens (human) ]

Gene ID: 54344, updated on 27-Nov-2024

Summary

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Official Symbol
DPM3provided by HGNC
Official Full Name
dolichyl-phosphate mannosyltransferase subunit 3, regulatoryprovided by HGNC
Primary source
HGNC:HGNC:3007
See related
Ensembl:ENSG00000179085 MIM:605951; AllianceGenome:HGNC:3007
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
CDG1O; MDDGB15; MDDGC15
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. The protein encoded by this gene is a subunit of dolichyl-phosphate mannosyltransferase and acts as a stabilizer subunit of the dolichyl-phosphate mannosyltransferase complex. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in fat (RPKM 20.5), colon (RPKM 20.2) and 25 other tissues See more
Orthologs
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Genomic context

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See DPM3 in Genome Data Viewer
Location:
1q22
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (155139891..155140531, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (154279249..154279889, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (155112367..155113007, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ephrin A1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1394 Neighboring gene solute carrier family 50 member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1808 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 18 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1395 Neighboring gene keratinocyte associated protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:155145543-155146051

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 recurrent homozygous missense DPM3 variant leads to muscle and brain disease. Nagy S, et al. Clin Genet, 2022 Dec. PMID 35932216, Free PMC Article
  2. Dolichol-phosphate-mannose-3 (DPM3)/prostin-1 is a novel phospholipase C-gamma regulated gene negatively associated with prostate tumor invasion. Manos EJ, et al. Oncogene, 2001 May 17. PMID 11420690
  3. Toward understanding tissue-specific symptoms in dolichol-phosphate-mannose synthesis disorders; insight from DPM3-CDG. van Tol W, et al. J Inherit Metab Dis, 2019 Sep. PMID 30931530
  4. 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
  5. PIG-M transfers the first mannose to glycosylphosphatidylinositol on the lumenal side of the ER. Maeda Y, et al. EMBO J, 2001 Jan 15. PMID 11226175, Free PMC Article

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A recurrent homozygous missense DPM3 variant leads to muscle and brain disease.
    Title: A recurrent homozygous missense DPM3 variant leads to muscle and brain disease.
  2. Toward understanding tissue-specific symptoms in dolichol-phosphate-mannose synthesis disorders; insight from DPM3-CDG.
    Title: Toward understanding tissue-specific symptoms in dolichol-phosphate-mannose synthesis disorders; insight from DPM3-CDG.
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

EBI GWAS Catalog

Description
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
EBI GWAS Catalog
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

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

  • MGC34275, MGC125904, MGC125905

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables enzyme activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in GPI anchor biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in GPI anchor biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in GPI anchor biosynthetic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in carbohydrate metabolic process NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in dolichol metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan TAS
Traceable Author Statement
more info
 PubMed 
involved_in protein O-linked mannosylation TAS
Traceable Author Statement
more info
 PubMed 
involved_in protein mannosylation TAS
Traceable Author Statement
more info
 PubMed 
involved_in regulation of protein stability IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
part_of dolichol-phosphate-mannose synthase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
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
 PubMed 
part_of mannosyltransferase complex TAS
Traceable Author Statement
more info
 PubMed 
located_in membrane HDA PubMed 

General protein information

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Preferred Names
dolichol-phosphate mannosyltransferase subunit 3
Names
DPM synthase complex subunit 3
DPM synthase subunit 3
MPD synthase subunit 3
dolichol-phosphate mannose synthase subunit 3
dolichyl-phosphate beta-D-mannosyltransferase subunit 3
dolichyl-phosphate mannosyltransferase polypeptide 3
mannose-P-dolichol synthase subunit 3
prostin 1
testicular tissue protein Li 58
NP_061846.2
NP_714963.1
XP_016856987.1
XP_054193079.1

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_012871.1 RefSeqGene

    Range
    4990..5630
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018973.4 → NP_061846.2  dolichol-phosphate mannosyltransferase subunit 3 isoform 1

    See identical proteins and their annotated locations for NP_061846.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL691442
    Consensus CDS
    CCDS1094.1
    UniProtKB/TrEMBL
    A0A140VJI4
    Related
    ENSP00000357384.1, ENST00000368399.1
    Conserved Domains (1) summary
    pfam08285
    Location:37 → 121
    DPM3; Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)

  2. NM_153741.2 → NP_714963.1  dolichol-phosphate mannosyltransferase subunit 3 isoform 2

    See identical proteins and their annotated locations for NP_714963.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR and 5' coding region, compared to variant 1. This results in translation initiation from a downstream ATG and an isoform (2) with a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AL691442
    Consensus CDS
    CCDS1095.1
    UniProtKB/Swiss-Prot
    Q5SR62, Q5SR63, Q9BXN4, Q9BXN5, Q9P2X0
    UniProtKB/TrEMBL
    Q86TM7
    Related
    ENSP00000357385.5, ENST00000368400.5
    Conserved Domains (1) summary
    pfam08285
    Location:1 → 90
    DPM3; Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    155139891..155140531 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017001498.2 → XP_016856987.1  dolichol-phosphate mannosyltransferase subunit 3 isoform X1

    UniProtKB/Swiss-Prot
    Q5SR62, Q5SR63, Q9BXN4, Q9BXN5, Q9P2X0
    UniProtKB/TrEMBL
    Q86TM7
    Related
    ENSP00000344338.3, ENST00000341298.3
    Conserved Domains (1) summary
    pfam08285
    Location:1 → 90
    DPM3; Dolichol-phosphate mannosyltransferase subunit 3 (DPM3)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    154279249..154279889 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337104.1 → XP_054193079.1  dolichol-phosphate mannosyltransferase subunit 3 isoform X1

    UniProtKB/Swiss-Prot
    Q5SR62, Q5SR63, Q9BXN4, Q9BXN5, Q9P2X0
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P2X0.2 GenPept UniProtKB/Swiss-Prot:Q9P2X0

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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