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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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See PLD4 in Genome Data Viewer
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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