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    PLD1 phospholipase D1 [ Homo sapiens (human) ]

    Gene ID: 5337, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See PLD1 in Genome Data Viewer
    Location:
    3q26.31
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (171600404..171810483, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (174384521..174594617, complement)
    RS_2024_09 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. Phosphatidic acid-producing enzymes regulating the synaptic vesicle cycle: Role for PLD? Barber CN, et al. Adv Biol Regul, 2018 Jan. PMID 28986032, Free PMC Article
    2. 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
    3. Requirement of phospholipase D1 activity in H-RasV12-induced transformation. Buchanan FG, et al. Proc Natl Acad Sci U S A, 2005 Feb 1. PMID 15668389, Free PMC Article
    4. Disruption of lipid rafts stimulates phospholipase d activity in human lymphocytes: implication in the regulation of immune function. Diaz O, et al. J Immunol, 2005 Dec 15. PMID 16339545
    5. 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

    See all (208) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A positive feedback loop between PLD1 and NF-kappaB signaling promotes tumorigenesis of nasopharyngeal carcinoma.
      Title: A positive feedback loop between PLD1 and NF-κB signaling promotes tumorigenesis of nasopharyngeal carcinoma.
    2. 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.
    3. 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.
    4. 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.
    5. Phospholipase D and cancer metastasis: A focus on exosomes.
      Title: Phospholipase D and cancer metastasis: A focus on exosomes.
    6. 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.
    7. Phospholipase D1 promotes cervical cancer progression by activating the RAS pathway.
      Title: Phospholipase D1 promotes cervical cancer progression by activating the RAS pathway.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (130)

    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
    		Compare labs

    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
    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 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 
    is_active_in cytoplasmic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 
    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
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    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_2024_08

    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
      UniProtKB/TrEMBL
      Q59EA4

    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

      UniProtKB/TrEMBL
      Q59EA4

    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
      UniProtKB/TrEMBL
      Q59EA4

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

      UniProtKB/Swiss-Prot
      Q13393
      UniProtKB/TrEMBL
      Q59EA4

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

      UniProtKB/TrEMBL
      Q59EA4

    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

      UniProtKB/TrEMBL
      Q59EA4

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

      UniProtKB/TrEMBL
      Q59EA4

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

      UniProtKB/TrEMBL
      Q59EA4

    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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