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    PLD4 phospholipase D family member 4 [ Homo sapiens (human) ]

    Gene ID: 122618, updated on 3-Apr-2024

    Summary

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    Official Symbol
    PLD4provided by HGNC
    Official Full Name
    phospholipase D family member 4provided by HGNC
    Primary source
    HGNC:HGNC:23792
    See related
    Ensembl:ENSG00000166428 MIM:618488; AllianceGenome:HGNC:23792
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C14orf175
    Summary
    Predicted to enable single-stranded DNA 5'-3' exodeoxyribonuclease activity. Predicted to be involved in hematopoietic progenitor cell differentiation; phagocytosis; and regulation of cytokine production involved in inflammatory response. Predicted to be located in early endosome and endoplasmic reticulum membrane. Predicted to be active in several cellular components, including endoplasmic reticulum; phagocytic vesicle; and trans-Golgi network membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in skin (RPKM 31.7), spleen (RPKM 4.6) and 9 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    14q32.33
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (104924879..104937785)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (99170773..99184262)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (105391216..105404122)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903397 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105332635-105333610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6205 Neighboring gene microRNA 12121 Neighboring gene centrosomal protein 170B Neighboring gene ReSE screen-validated silencer GRCh37_chr14:105342668-105342853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105343537-105344095 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105347753-105348661 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105348662-105349569 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105372467-105373090 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:105381788-105382013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9125 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_33759 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105391541-105392050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105398641-105399539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105405832-105406332 Neighboring gene AHNAK nucleoprotein 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_33767 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105433703-105434436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105435172-105435905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6209 Neighboring gene clathrin binding box of aftiphilin containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105485485-105486145 Neighboring gene H3K27ac hESC enhancers GRCh37_chr14:105486597-105487112 and GRCh37_chr14:105487627-105488140 Neighboring gene cell division cycle associated 4

    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. PLD4 promotes M1 macrophages to perform antitumor effects in colon cancer cells. Gao L, et al. Oncol Rep, 2017 Jan. PMID 27840999
    2. PLD4 as a novel susceptibility gene for systemic sclerosis in a Japanese population. Terao C, et al. Arthritis Rheum, 2013 Feb. PMID 23124809
    3. PLD4 is a genetic determinant to systemic lupus erythematosus and involved in murine autoimmune phenotypes. Akizuki S, et al. Ann Rheum Dis, 2019 Apr. PMID 30679154
    4. Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population. Okada Y, et al. Nat Genet, 2012 Mar 25. PMID 22446963
    5. Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Tao WA, et al. Nat Methods, 2005 Aug. PMID 16094384

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Phospholipase D4 as a signature of toll-like receptor 7 or 9 signaling is expressed on blastic T-bet + B cells in systemic lupus erythematosus.
      Title: Phospholipase D4 as a signature of toll-like receptor 7 or 9 signaling is expressed on blastic T-bet + B cells in systemic lupus erythematosus.
    2. PLD4 is a genetic determinant to systemic lupus erythematosus.
      Title: PLD4 is a genetic determinant to systemic lupus erythematosus and involved in murine autoimmune phenotypes.
    3. PLD4 expression in colon cancer tissues
      Title: PLD4 promotes M1 macrophages to perform antitumor effects in colon cancer cells.
    4. We determined that PLD4 is a novel susceptibility gene for sysetmic sclerosis in Japanese, thus confirming the involvement of PLD4 in autoimmunity.
      Title: PLD4 as a novel susceptibility gene for systemic sclerosis in a Japanese population.
    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
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables phospholipase D activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables single-stranded DNA 5'-3' DNA exonuclease activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in establishment of localization in cell IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in hematopoietic progenitor cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phagocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within phagocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cytokine production involved in inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in early endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in phagocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in phagocytic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in trans-Golgi network membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    5'-3' exonuclease PLD4
    Names
    PLD 4
    choline phosphatase 4
    phosphatidylcholine-hydrolyzing phospholipase D4
    phospholipase D4
    NP_001295103.1
    NP_620145.2
    XP_011534713.1
    XP_054231322.1

    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.

    mRNA and Protein(s)

    1. NM_001308174.2 → NP_001295103.1  5'-3' exonuclease PLD4 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK295352, AK296188, AL512802, AW104909, DC328186
      Consensus CDS
      CCDS76725.1
      UniProtKB/TrEMBL
      B4DJQ6, F5H2B5
      Related
      ENSP00000438677.1, ENST00000540372.5
      Conserved Domains (3) summary
      cd09145
      Location:105 → 274
      PLDc_vPLD4_1; Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4
      cd09148
      Location:311 → 497
      PLDc_vPLD4_2; Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4
      PHA02820
      Location:99 → 509
      PHA02820; phospholipase-D-like protein; Provisional

    2. NM_138790.5 → NP_620145.2  5'-3' exonuclease PLD4 isoform 2

      See identical proteins and their annotated locations for NP_620145.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and uses an alternate splice site in the 5' coding region that results in use of a downstream start codon compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AY358843
      Consensus CDS
      CCDS9995.2
      UniProtKB/Swiss-Prot
      Q6UWD2, Q96BZ4
      UniProtKB/TrEMBL
      B4DI07
      Related
      ENSP00000376372.5, ENST00000392593.9
      Conserved Domains (3) summary
      cd09148
      Location:304 → 490
      PLDc_vPLD4_2; Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4
      PHA02820
      Location:92 → 502
      PHA02820; phospholipase-D-like protein; Provisional
      cl15239
      Location:98 → 267
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      104924879..104937785
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011536411.3 → XP_011534713.1  5'-3' exonuclease PLD4 isoform X1

      UniProtKB/TrEMBL
      A0A3B3IT68
      Related
      ENSP00000497627.1, ENST00000649344.1
      Conserved Domains (4) summary
      cd09145
      Location:105 → 274
      PLDc_vPLD4_1; Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4
      COG1502
      Location:218 → 440
      Cls; Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase or related enzyme [Lipid transport and metabolism]
      pfam13091
      Location:130 → 272
      PLDc_2; PLD-like domain
      cl15239
      Location:311 → 447
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      99170773..99184262
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375347.1 → XP_054231322.1  5'-3' exonuclease PLD4 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96BZ4.2 GenPept UniProtKB/Swiss-Prot:Q96BZ4

    Gene LinkOut

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