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PLD1 phospholipase D1 [ Homo sapiens (human) ]

Gene ID: 5337, updated on 3-Apr-2024

Summary

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Official Symbol
PLD1provided by HGNC
Official Full Name
phospholipase D1provided by HGNC
Primary source
HGNC:HGNC:9067
See related
Ensembl:ENSG00000075651 MIM:602382; AllianceGenome:HGNC:9067
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
CVDD; CVDP1
Summary
This gene encodes a phosphatidylcholine-specific phospholipase which catalyzes the hydrolysis of phosphatidylcholine in order to yield phosphatidic acid and choline. The enzyme may play a role in signal transduction and subcellular trafficking. Alternative splicing results in multiple transcript variants with both catalytic and regulatory properties. [provided by RefSeq, Sep 2011]
Expression
Ubiquitous expression in gall bladder (RPKM 28.0), duodenum (RPKM 12.6) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
3q26.31
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (171600404..171810483, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (174384521..174594617, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (171318194..171528273, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 348, pseudogene Neighboring gene Sharpr-MPRA regulatory region 12788 Neighboring gene MT-CO1 pseudogene 58 Neighboring gene small nucleolar RNA U13 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:171436449-171437034 Neighboring gene Sharpr-MPRA regulatory region 14633 Neighboring gene transmembrane protein 212 Neighboring gene TMEM212 antisense RNA 1 Neighboring gene uncharacterized LOC105374218

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. Phospholipase D1 promotes cervical cancer progression by activating the RAS pathway. Song M, et al. J Cell Mol Med, 2022 Aug. PMID 35775110, Free PMC Article
  2. Phospholipase D1-generated phosphatidic acid modulates secretory granule trafficking from biogenesis to compensatory endocytosis in neuroendocrine cells. Tanguy E, et al. Adv Biol Regul, 2022 Jan. PMID 34876384
  3. Biallelic loss-of-function variants in PLD1 cause congenital right-sided cardiac valve defects and neonatal cardiomyopathy. Lahrouchi N, et al. J Clin Invest, 2021 Mar 1. PMID 33645542, Free PMC Article
  4. Phospholipase D1 is upregulated by vorinostat and confers resistance to vorinostat in glioblastoma. Kang DW, et al. J Cell Physiol, 2021 Jan. PMID 32869317, Free PMC Article
  5. Roles for Phospholipase D1 in the Tumor Microenvironment. Barisano D, et al. Adv Exp Med Biol, 2020. PMID 32578172

See all (200) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Lipopolysaccharide Stimulates A549 Cell Migration through p-Tyr 42 RhoA and Phospholipase D1 Activity.
    Title: Lipopolysaccharide Stimulates A549 Cell Migration through p-Tyr 42 RhoA and Phospholipase D1 Activity.
  2. Nuclear PLD1 combined with NPM1 induces gemcitabine resistance through tumorigenic IL7R in pancreatic adenocarcinoma.
    Title: Nuclear PLD1 combined with NPM1 induces gemcitabine resistance through tumorigenic IL7R in pancreatic adenocarcinoma.
  3. Raf/MEK/ERK Signaling Pathway Is Involved in the Inhibition of Glioma Cell Proliferation and Invasion in the Ketogenic Microenvironment.
    Title: Raf/MEK/ERK Signaling Pathway Is Involved in the Inhibition of Glioma Cell Proliferation and Invasion in the Ketogenic Microenvironment.
  4. Phospholipase D and cancer metastasis: A focus on exosomes.
    Title: Phospholipase D and cancer metastasis: A focus on exosomes.
  5. Exosome Secretion and Epithelial-Mesenchymal Transition in Ovarian Cancer Are Regulated by Phospholipase D.
    Title: Exosome Secretion and Epithelial-Mesenchymal Transition in Ovarian Cancer Are Regulated by Phospholipase D.
  6. Phospholipase D1 promotes cervical cancer progression by activating the RAS pathway.
    Title: Phospholipase D1 promotes cervical cancer progression by activating the RAS pathway.
  7. Phospholipase D1-generated phosphatidic acid modulates secretory granule trafficking from biogenesis to compensatory endocytosis in neuroendocrine cells.
    Title: Phospholipase D1-generated phosphatidic acid modulates secretory granule trafficking from biogenesis to compensatory endocytosis in neuroendocrine cells.
  8. PLD1 knockdown reduces metastasis and inflammation of fibroblast-like synoviocytes in rheumatoid arthritis by modulating NF-kappaB and Wnt/beta-catenin pathways.
    Title: PLD1 knockdown reduces metastasis and inflammation of fibroblast-like synoviocytes in rheumatoid arthritis by modulating NF-κB and Wnt/β-catenin pathways.
  9. RalA and PLD1 promote lipid droplet growth in response to nutrient withdrawal.
    Title: RalA and PLD1 promote lipid droplet growth in response to nutrient withdrawal.
  10. Click chemistry-enabled CRISPR screening reveals GSK3 as a regulator of PLD signaling.
    Title: Click chemistry-enabled CRISPR screening reveals GSK3 as a regulator of PLD signaling.
Submit: New GeneRIF Correction See all GeneRIFs (129)

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
Cardiac valvular defect, developmental
MedGen: C5774175 OMIM: 212093 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)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
HIV-1 replication requires PLD1 as shown through specific PLD1 inhibitors in activated CD4+ T cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120-induced phosphatidylcholine-specific phospholipase D (PLD) activity is dependent on the activation of ERK1/2 PubMed
Tat tat Microarray analysis indicates HIV-1 Tat-induced upregulation of phosphatidylcholine-specific phospholipase D1 (PLD1) in primary human brain microvascular endothelial 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 N-acylphosphatidylethanolamine-specific phospholipase D activity IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol binding IEA
Inferred from Electronic Annotation
more info
  
enables phospholipase D activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phospholipase D activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phospholipase D activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Ras protein signal transduction TAS
Traceable Author Statement
more info
  
involved_in cellular response to nutrient IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chemotaxis TAS
Traceable Author Statement
more info
  
involved_in phosphatidic acid biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in phospholipid catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of translation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of microvillus assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of microvillus assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of synaptic vesicle cycle IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of synaptic vesicle cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in small GTPase-mediated signal transduction TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
located_in apical plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cholinergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cholinergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in endocytic vesicle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in endosome IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in late endosome membrane IEA
Inferred from Electronic Annotation
more info
  
located_in lysosomal membrane HDA PubMed 
located_in membrane HDA PubMed 
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
is_active_in plasma membrane region IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in specific granule membrane TAS
Traceable Author Statement
more info
  
located_in tertiary granule membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
phospholipase D1
Names
choline phosphatase 1
phosphatidylcholine-hydrolyzing phospholipase D1
phospholipase D1, phosphatidylcholine-specific
NP_001123553.1
NP_002653.1
XP_005247590.1
XP_005247591.1
XP_011511199.1
XP_011511200.1
XP_011511201.1
XP_016862113.1
XP_047304272.1
XP_047304273.1
XP_047304274.1
XP_054202834.1
XP_054202835.1
XP_054202836.1
XP_054202837.1
XP_054202838.1
XP_054202839.1
XP_054202840.1
XP_054202841.1
XP_054202842.1

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_029851.1 RefSeqGene

    Range
    5012..215091
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130081.3 → NP_001123553.1  phospholipase D1 isoform b

    See identical proteins and their annotated locations for NP_001123553.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region, compared to variant 1. The resulting isoform (b) has the same N- and C-termini, but is shorter compared to isoform a.
    Source sequence(s)
    AB209907, AC008134, DA464847
    Consensus CDS
    CCDS46957.1
    UniProtKB/TrEMBL
    Q59EA4
    Related
    ENSP00000348681.5, ENST00000356327.9
    Conserved Domains (5) summary
    cd07296
    Location:78 → 209
    PX_PLD1; The phosphoinositide binding Phox Homology domain of Phospholipase D1
    cd09842
    Location:352 → 502
    PLDc_vPLD1_1; Catalytic domain, repeat 1, of vertebrate phospholipase D1
    cd09844
    Location:716 → 897
    PLDc_vPLD1_2; Catalytic domain, repeat 2, of vertebrate phospholipase D1
    PLN02866
    Location:82 → 1021
    PLN02866; phospholipase D
    cd01254
    Location:197 → 326
    PH_PLD; Phospholipase D pleckstrin homology (PH) domain

  2. NM_002662.5 → NP_002653.1  phospholipase D1 isoform a

    See identical proteins and their annotated locations for NP_002653.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AB209907, AC008134, BC068976, DA464847
    Consensus CDS
    CCDS3216.1
    UniProtKB/Swiss-Prot
    Q13393
    UniProtKB/TrEMBL
    Q59EA4
    Related
    ENSP00000342793.4, ENST00000351298.9
    Conserved Domains (1) summary
    cl26365
    Location:82 → 1059
    PLN03008; Phospholipase D delta

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    171600404..171810483 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047448316.1 → XP_047304272.1  phospholipase D1 isoform X1

    UniProtKB/Swiss-Prot
    Q13393

  2. XM_005247534.3 → XP_005247591.1  phospholipase D1 isoform X2

    See identical proteins and their annotated locations for XP_005247591.1

    UniProtKB/TrEMBL
    Q59EA4
    Conserved Domains (5) summary
    cd07296
    Location:78 → 209
    PX_PLD1; The phosphoinositide binding Phox Homology domain of Phospholipase D1
    cd09842
    Location:352 → 502
    PLDc_vPLD1_1; Catalytic domain, repeat 1, of vertebrate phospholipase D1
    cd09844
    Location:716 → 897
    PLDc_vPLD1_2; Catalytic domain, repeat 2, of vertebrate phospholipase D1
    PLN02866
    Location:82 → 1021
    PLN02866; phospholipase D
    cd01254
    Location:197 → 326
    PH_PLD; Phospholipase D pleckstrin homology (PH) domain

  3. XM_005247533.3 → XP_005247590.1  phospholipase D1 isoform X1

    See identical proteins and their annotated locations for XP_005247590.1

    UniProtKB/Swiss-Prot
    Q13393
    UniProtKB/TrEMBL
    Q59EA4
    Conserved Domains (1) summary
    cl26365
    Location:82 → 1059
    PLN03008; Phospholipase D delta

  4. XM_047448318.1 → XP_047304274.1  phospholipase D1 isoform X6

  5. XM_011512899.3 → XP_011511201.1  phospholipase D1 isoform X7

    Conserved Domains (3) summary
    cd09844
    Location:337 → 518
    PLDc_vPLD1_2; Catalytic domain, repeat 2, of vertebrate phospholipase D1
    pfam13091
    Location:349 → 520
    PLDc_2; PLD-like domain
    cl15239
    Location:1 → 85
    PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

  6. XM_017006624.2 → XP_016862113.1  phospholipase D1 isoform X7

    Conserved Domains (3) summary
    cd09844
    Location:337 → 518
    PLDc_vPLD1_2; Catalytic domain, repeat 2, of vertebrate phospholipase D1
    pfam13091
    Location:349 → 520
    PLDc_2; PLD-like domain
    cl15239
    Location:1 → 85
    PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

  7. XM_011512898.2 → XP_011511200.1  phospholipase D1 isoform X4

    UniProtKB/TrEMBL
    Q59EA4
    Conserved Domains (6) summary
    cd07296
    Location:78 → 209
    PX_PLD1; The phosphoinositide binding Phox Homology domain of Phospholipase D1
    cd09842
    Location:352 → 502
    PLDc_vPLD1_1; Catalytic domain, repeat 1, of vertebrate phospholipase D1
    cd09844
    Location:754 → 935
    PLDc_vPLD1_2; Catalytic domain, repeat 2, of vertebrate phospholipase D1
    cd01254
    Location:197 → 326
    PH_PLD; Phospholipase D pleckstrin homology (PH) domain
    pfam00169
    Location:222 → 327
    PH; PH domain
    pfam13091
    Location:766 → 937
    PLDc_2; PLD-like domain

  8. XM_047448317.1 → XP_047304273.1  phospholipase D1 isoform X5

  9. XM_011512897.2 → XP_011511199.1  phospholipase D1 isoform X3

    See identical proteins and their annotated locations for XP_011511199.1

    UniProtKB/TrEMBL
    Q59EA4
    Conserved Domains (6) summary
    cd07296
    Location:78 → 209
    PX_PLD1; The phosphoinositide binding Phox Homology domain of Phospholipase D1
    cd09842
    Location:352 → 502
    PLDc_vPLD1_1; Catalytic domain, repeat 1, of vertebrate phospholipase D1
    cd09844
    Location:754 → 935
    PLDc_vPLD1_2; Catalytic domain, repeat 2, of vertebrate phospholipase D1
    cd01254
    Location:197 → 326
    PH_PLD; Phospholipase D pleckstrin homology (PH) domain
    pfam00169
    Location:222 → 327
    PH; PH domain
    pfam13091
    Location:766 → 937
    PLDc_2; PLD-like domain

RNA

  1. XR_007095693.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    174384521..174594617 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054346860.1 → XP_054202835.1  phospholipase D1 isoform X1

    UniProtKB/Swiss-Prot
    Q13393

  2. XM_054346859.1 → XP_054202834.1  phospholipase D1 isoform X1

    UniProtKB/Swiss-Prot
    Q13393

  3. XM_054346861.1 → XP_054202836.1  phospholipase D1 isoform X2

  4. XM_054346865.1 → XP_054202840.1  phospholipase D1 isoform X6

  5. XM_054346867.1 → XP_054202842.1  phospholipase D1 isoform X7

  6. XM_054346866.1 → XP_054202841.1  phospholipase D1 isoform X7

  7. XM_054346863.1 → XP_054202838.1  phospholipase D1 isoform X4

  8. XM_054346862.1 → XP_054202837.1  phospholipase D1 isoform X3

  9. XM_054346864.1 → XP_054202839.1  phospholipase D1 isoform X5

RNA

  1. XR_008486735.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13393.1 GenPept UniProtKB/Swiss-Prot:Q13393

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