Aliases for PLD4 Gene

Aliases for PLD4 Gene

  • Phospholipase D Family Member 4 2 3 4 5
  • Phosphatidylcholine-Hydrolyzing Phospholipase D4 3 4
  • 5'-3' Exonuclease PLD4 3 4
  • Choline Phosphatase 4 3 4
  • Phospholipase D4 3 4
  • C14orf175 3 4
  • PLD 4 3 4
  • Chromosome 14 Open Reading Frame 175 2
  • Phospholipase D Family, Member 4 2
  • EC 3.1.16.1 4
  • EC 3.1.4.4 50
  • PLD4 5

External Ids for PLD4 Gene

Previous HGNC Symbols for PLD4 Gene

  • C14orf175

Previous GeneCards Identifiers for PLD4 Gene

  • GC14P104464
  • GC14P105391
  • GC14P085585

Summaries for PLD4 Gene

GeneCards Summary for PLD4 Gene

PLD4 (Phospholipase D Family Member 4) is a Protein Coding gene. Diseases associated with PLD4 include Nephrotic Syndrome, Type 7 and Doyne Honeycomb Retinal Dystrophy. Among its related pathways are Glycerophospholipid biosynthesis and Metabolism. Gene Ontology (GO) annotations related to this gene include phosphatidylinositol phospholipase C activity and N-acylphosphatidylethanolamine-specific phospholipase D activity. An important paralog of this gene is PLD3.

UniProtKB/Swiss-Prot Summary for PLD4 Gene

  • 5'->3' DNA exonuclease which digests single-stranded DNA (ssDNA). Regulates inflammatory cytokine responses via the degradation of nucleic acids, by reducing the concentration of ssDNA able to stimulate TLR9, a nucleotide-sensing receptor. Involved in phagocytosis of activated microglia.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PLD4 Gene

Genomics for PLD4 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PLD4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14J104924 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 250.7 +1.7 1748 2.7 BCLAF1 SP1 ZNF207 ZIC2 BCL11A TRIM22 IRF4 EBF1 CBFB SMARCA5 lnc-AHNAK2-1 lnc-AHNAK2-2 lnc-AHNAK2-3 lnc-AHNAK2-4 PLD4 CLBA1 CEP170B AHNAK2
GH14J104922 Enhancer 0.3 Ensembl 250.7 -1.6 -1600 0.2 EBF1 PLD4 CEP170B HSALNG0104164
GH14J104882 Enhancer 1 Ensembl ENCODE dbSUPER 11.9 -42.3 -42345 2.1 SP2 PRDM10 MAZ GLIS1 ZNF18 ZFP69B KLF1 SP3 MNT EGR2 CEP170B PLD4 lnc-AHNAK2-5 HSALNG0104158
GH14J104656 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 5.4 -264.9 -264914 6.8 BCLAF1 SP1 CEBPA NFIC ZIC2 BCL11A ZNF592 ZNF341 ZNF623 RXRA C14orf180 TMEM179 PLD4 INF2 HSALNG0104116 lnc-INF2-2 LINC02280
GH14J105257 Enhancer 0.6 Ensembl ENCODE dbSUPER 9.9 +333.4 333400 1 KLF1 PACS2 BRF1 NUDT14 JAG2 CLBA1 PLD4 BTBD6 RF00017-1533 lnc-BTBD6-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PLD4 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PLD4

Top Transcription factor binding sites by QIAGEN in the PLD4 gene promoter:
  • AML1a
  • Arnt
  • ARP-1
  • c-Myc
  • C/EBPalpha
  • Max1
  • p53
  • Pax-4a
  • RP58

Genomic Locations for PLD4 Gene

Latest Assembly
chr14:104,924,301-104,937,789
(GRCh38/hg38)
Size:
13,489 bases
Orientation:
Plus strand

Previous Assembly
chr14:105,391,216-105,404,122
(GRCh37/hg19 by Entrez Gene)
Size:
12,907 bases
Orientation:
Plus strand

chr14:105,391,153-105,399,574
(GRCh37/hg19 by Ensembl)
Size:
8,422 bases
Orientation:
Plus strand

Genomic View for PLD4 Gene

Genes around PLD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLD4 Gene

Proteins for PLD4 Gene

  • Protein details for PLD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96BZ4-PLD4_HUMAN
    Recommended name:
    5'-3' exonuclease PLD4
    Protein Accession:
    Q96BZ4
    Secondary Accessions:
    • Q6UWD2

    Protein attributes for PLD4 Gene

    Size:
    506 amino acids
    Molecular mass:
    55626 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAQ89202.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for PLD4 Gene

Selected DME Specific Peptides for PLD4 Gene

Q96BZ4:
  • DNALRAAA
  • GSANMDW

Post-translational modifications for PLD4 Gene

  • Highly N-glycosylated.
  • Glycosylation at Asn150, Asn171, Asn249, Asn281, Asn403, Asn417, Asn427, and Asn444
  • Ubiquitination at Lys271 and Lys276
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Domains & Families for PLD4 Gene

Gene Families for PLD4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for PLD4 Gene

InterPro:
Blocks:
  • Phospholipase D/viral envelope

Suggested Antigen Peptide Sequences for PLD4 Gene

GenScript: Design optimal peptide antigens:
  • Phosphatidylcholine-hydrolyzing phospholipase D4 (PLD4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96BZ4

UniProtKB/Swiss-Prot:

PLD4_HUMAN :
  • Belongs to the phospholipase D family.
Family:
  • Belongs to the phospholipase D family.
genes like me logo Genes that share domains with PLD4: view

Function for PLD4 Gene

Molecular function for PLD4 Gene

UniProtKB/Swiss-Prot Function:
5'->3' DNA exonuclease which digests single-stranded DNA (ssDNA). Regulates inflammatory cytokine responses via the degradation of nucleic acids, by reducing the concentration of ssDNA able to stimulate TLR9, a nucleotide-sensing receptor. Involved in phagocytosis of activated microglia.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 3'-phosphates.; EC=3.1.16.1; Evidence={ECO:0000250|UniProtKB:Q8BG07};.

Enzyme Numbers (IUBMB) for PLD4 Gene

Phenotypes From GWAS Catalog for PLD4 Gene

Gene Ontology (GO) - Molecular Function for PLD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004518 nuclease activity IEA --
GO:0004527 exonuclease activity IEA --
GO:0004630 NOT phospholipase D activity ISS --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with PLD4: view
genes like me logo Genes that share phenotypes with PLD4: view

Animal Models for PLD4 Gene

MGI Knock Outs for PLD4:
  • Pld4 Pld4<tm1.2Nemz>

Animal Models for research

  • Taconic Biosciences Mouse Models for PLD4

miRNA for PLD4 Gene

miRTarBase miRNAs that target PLD4

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PLD4

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PLD4 Gene

Localization for PLD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLD4 Gene

Endoplasmic reticulum membrane. Single-pass type II membrane protein. Golgi apparatus, trans-Golgi network membrane. Single-pass type II membrane protein. Nucleus. Early endosome. Cytoplasmic vesicle, phagosome. Note=Activation of microglia induces translocation of PLD4 from the nucleus to the phagosomes. {ECO:0000250 UniProtKB:Q8BG07}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PLD4 gene
Compartment Confidence
nucleus 4
endoplasmic reticulum 4
endosome 4
golgi apparatus 4
mitochondrion 2
plasma membrane 1
extracellular 1
cytoskeleton 1
lysosome 1
cytosol 0

Gene Ontology (GO) - Cellular Components for PLD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,ISS --
GO:0005768 endosome IEA --
GO:0005769 early endosome ISS --
GO:0005783 endoplasmic reticulum IBA 21873635
GO:0005789 endoplasmic reticulum membrane TAS --
genes like me logo Genes that share ontologies with PLD4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PLD4 Gene

Pathways & Interactions for PLD4 Gene

genes like me logo Genes that share pathways with PLD4: view

Interacting Proteins for PLD4 Gene

Gene Ontology (GO) - Biological Process for PLD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002244 hematopoietic progenitor cell differentiation IBA 21873635
GO:0002376 immune system process IEA --
GO:0006259 DNA metabolic process IEA --
GO:0006909 phagocytosis IBA,ISS --
GO:0006954 inflammatory response IEA --
genes like me logo Genes that share ontologies with PLD4: view

No data available for SIGNOR curated interactions for PLD4 Gene

Drugs & Compounds for PLD4 Gene

(5) Drugs for PLD4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Choline Approved Nutra 240
Ethanolamine Experimental Pharma 0
L-Dilinoleoyllecithin Experimental Pharma 0
PE(16:0/16:0) Experimental Pharma 0

(15) Additional Compounds for PLD4 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Beta-Cortolone
  • 1-Palmityl-2-palmitoleoyl-sn-glycero-3-phosphocholine
  • Gpcho(16:0/16:1)
  • Gpcho(16:0/16:1n7)
  • Gpcho(16:0/16:1W7)
  • Gpcho(32:1)
CE(22:0)
  • 1-Tetradecanoyl-2-octadecanoyl-sn-glycero-3-phosphocholine
  • GPCho(14:0/18:0)
  • Phosphatidylcholine(14:0/18:0)
  • 1-Myristoyl-2-stearoylphosphatidylcholine
  • 1m-2S-PC
61510-09-6
Hydroxyclomipramine
  • 1-(1Z-Octadecenyl)-2-(5Z,8Z,11Z,14Z- eicosatetraenoyl)-sn-glycero-3-phosphoethanolamine
  • 1-(1Z-Octadecenyl)-2-(5Z,8Z,11Z,14Z-icosatetraenoyl)-sn-glycero-3-phosphoethanolamine zwitterion
  • 1-(1-Enyl-stearoyl)-2-arachidonoyl-sn-glycero-3-phosphoethanolamine
  • 1-(1Z-Octadecenyl)-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphoethanolamine
  • 1-Alkenyl-2-acyl-glycerophosphoethanolamine
97859-69-3
LysoPE(P-16:0/0:0)
  • 1-(1Z-Hexadecenyl)-lysophosphatidylethanolamine
  • 1-(1Z-Hexadecenyl)-sn-glycero-3-phosphoethanolamine
  • LPE(16:1)
  • LPE(p-16:0)
  • LPE(p-16:0/0:0)
174062-72-7
PC(18:1(9Z)e/2:0)
  • (2-Acetyloxy-3-octadec-9-enoxypropyl) 2-trimethylazaniumylethyl phosphate
  • 2-Acetyl-1-(9Z-octadecenyl)-sn-glycero-3-phosphocholine
  • PC(O-18:1(9Z)/2:0)
genes like me logo Genes that share compounds with PLD4: view

Transcripts for PLD4 Gene

mRNA/cDNA for PLD4 Gene

2 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PLD4

Alternative Splicing Database (ASD) splice patterns (SP) for PLD4 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9a · 9b ^ 10 ^ 11
SP1: - -
SP2: - -
SP3: - - -
SP4:
SP5:

Relevant External Links for PLD4 Gene

GeneLoc Exon Structure for
PLD4

Expression for PLD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PLD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PLD4 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x7.3), Brain - Substantia nigra (x5.3), and Spleen (x4.2).

Protein differential expression in normal tissues from HIPED for PLD4 Gene

This gene is overexpressed in Lymph node (36.1), Blymphocyte (13.0), Plasma (7.0), and Monocytes (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PLD4 Gene



Protein tissue co-expression partners for PLD4 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PLD4

SOURCE GeneReport for Unigene cluster for PLD4 Gene:

Hs.407101
genes like me logo Genes that share expression patterns with PLD4: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PLD4 Gene

Orthologs for PLD4 Gene

This gene was present in the common ancestor of animals.

Orthologs for PLD4 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PLD4 29
  • 98.53 (n)
Dog
(Canis familiaris)
Mammalia PLD4 29 30
  • 84.99 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PLD4 29 30
  • 82.35 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pld4 29
  • 79.11 (n)
Mouse
(Mus musculus)
Mammalia Pld4 29 16 30
  • 78.7 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PLD4 30
  • 62 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PLD4 30
  • 59 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PLD4 29 30
  • 59.2 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PLD4 30
  • 49 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii si:dkeyp-110e4.6 29
  • 53.53 (n)
PLD4 (2 of 2) 30
  • 50 (a)
OneToMany
PLD4 (1 of 2) 30
  • 47 (a)
OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8932 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG9248 30
  • 34 (a)
ManyToMany
CG43345 30
  • 33 (a)
ManyToMany
Worm
(Caenorhabditis elegans)
Secernentea T05C3.6 29
  • 44.75 (n)
Y51A2D.13 30
  • 27 (a)
ManyToMany
E04F6.4 30
  • 18 (a)
ManyToMany
Species where no ortholog for PLD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for PLD4 Gene

ENSEMBL:
Gene Tree for PLD4 (if available)
TreeFam:
Gene Tree for PLD4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PLD4: view image
Alliance of Genome Resources:
Additional Orthologs for PLD4

Paralogs for PLD4 Gene

Paralogs for PLD4 Gene

(3) SIMAP similar genes for PLD4 Gene using alignment to 4 proteins:

  • PLD4_HUMAN
  • F5H2B5_HUMAN
  • G3V3J8_HUMAN
  • G3V472_HUMAN
genes like me logo Genes that share paralogs with PLD4: view

Variants for PLD4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PLD4 Gene

SNP ID Clinical significance and condition Chr 14 pos Variation AA Info Type
rs375062151 Likely Benign: not provided 104,928,936(+) C/T
NM_138790.5(PLD4):c.468+4C>T
INTRON
rs2841280 -- p.Glu27Gln
rs3803295 -- p.Val135Met
rs894037 -- p.Cys16Arg

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PLD4 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PLD4 Gene

Variant ID Type Subtype PubMed ID
nsv1049253 CNV gain 25217958
nsv1054574 CNV loss 25217958
nsv566099 CNV gain 21841781
nsv566139 CNV loss 21841781
nsv952276 CNV deletion 24416366

Variation tolerance for PLD4 Gene

Residual Variation Intolerance Score: 55.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.11; 75.53% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PLD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLD4
Leiden Open Variation Database (LOVD)
PLD4

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLD4 Gene

Disorders for PLD4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PLD4 Gene - From: COP

Disorder Aliases PubMed IDs
nephrotic syndrome, type 7
  • nphs7
doyne honeycomb retinal dystrophy
  • dhrd
- elite association - COSMIC cancer census association via MalaCards
Search PLD4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PLD4

genes like me logo Genes that share disorders with PLD4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PLD4 Gene

Publications for PLD4 Gene

  1. Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population. (PMID: 22446963) Okada Y … Yamamoto K (Nature genetics 2012) 3 40
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4
  4. BCAR1 promotes proliferation and cell growth in lung adenocarcinoma via upregulation of POLR2A. (PMID: 33001583) Mao CG … Deng B (Thoracic cancer 2020) 3
  5. PLD4 is a genetic determinant to systemic lupus erythematosus and involved in murine autoimmune phenotypes. (PMID: 30679154) Akizuki S … Terao C (Annals of the rheumatic diseases 2019) 3

Products for PLD4 Gene

Sources for PLD4 Gene