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Aliases for PLD3 Gene

Aliases for PLD3 Gene

  • Phospholipase D Family Member 3 2 3 5
  • Phosphatidylcholine-Hydrolyzing Phospholipase D3 3 4
  • Choline Phosphatase 3 3 4
  • HindIII K4L Homolog 3 4
  • Phospholipase D3 2 3
  • EC 3.1.4.4 4 61
  • HU-K4 3 4
  • Phospholipase D Family, Member 3 2
  • EC 3.1.4 61
  • PLD 3 4
  • AD19 3
  • HUK4 3

External Ids for PLD3 Gene

Previous GeneCards Identifiers for PLD3 Gene

  • GC19P041505
  • GC19P041257
  • GC19P045530
  • GC19P045546
  • GC19P045557
  • GC19P040854
  • GC19P037290

Summaries for PLD3 Gene

Entrez Gene Summary for PLD3 Gene

  • This gene encodes a member of the phospholipase D (PLD) family of enzymes that catalyze the hydrolysis of membrane phospholipids. The encoded protein is a single-pass type II membrane protein and contains two PLD phosphodiesterase domains. This protein influences processing of amyloid-beta precursor protein. Mutations in this gene are associated with Alzheimer disease risk. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Apr 2014]

GeneCards Summary for PLD3 Gene

PLD3 (Phospholipase D Family Member 3) is a Protein Coding gene. Diseases associated with PLD3 include Alzheimer Disease 19, Late Onset and Acute Conjunctivitis. Among its related pathways are Metabolism and Immune System. GO annotations related to this gene include phospholipase D activity and N-acylphosphatidylethanolamine-specific phospholipase D activity. An important paralog of this gene is PLD4.

UniProtKB/Swiss-Prot for PLD3 Gene

  • May be involved in APP processing.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLD3 Gene

Genomics for PLD3 Gene

Regulatory Elements for PLD3 Gene

Enhancers for PLD3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19F040347 0.5 ENCODE 13.9 +0.2 160 2.2 HDGF PKNOX1 CREB3L1 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 SNRPA ENSG00000269843 FBL ENSG00000205041 ENSG00000269069 CCDC97 RN7SL566P COQ8B ITPKC RPS16
GH19F040340 1.2 FANTOM5 Ensembl ENCODE 12.5 -6.2 -6221 3.3 CTCF FEZF1 ZEB2 RAD21 ZEB1 ZNF121 JUND ZNF366 GLIS1 ZNF747 PLD3 ENSG00000269843 SNRPA PSMC4 C19orf47 SERTAD3 ENSG00000207281 GC19P040343
GH19F040304 0.2 ENCODE 11.7 -44.3 -44347 0.1 ZNF362 ATF1 ZNF366 SCRT2 NFE2 KDM1A MLLT1 ZBTB33 ENSG00000206925 C19orf47 PLD3 SERTAD1 SERTAD3 HIPK4 TTC9B CNTD2 SHKBP1 GC19M040298
GH19F040302 0.4 ENCODE 11.7 -46.1 -46057 0.2 ZNF362 GLIS1 PRDM10 BCL11B ENSG00000206925 C19orf47 PLD3 SERTAD1 SERTAD3 HIPK4 TTC9B CNTD2 SHKBP1 GC19M040298
GH19F040330 0.5 ENCODE 11.4 -17.1 -17105 1.2 ZNF362 CEBPB ZNF501 CEBPG ZFHX2 GATA3 ZSCAN16 WT1 EGR2 PLD3 C19orf47 ENSG00000207281 GC19M040298
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PLD3 on UCSC Golden Path with GeneCards custom track

Promoters for PLD3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000346584 75 2600 HDGF PKNOX1 CREB3L1 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for PLD3 Gene

Chromosome:
19
Start:
40,348,425 bp from pter
End:
40,380,439 bp from pter
Size:
32,015 bases
Orientation:
Plus strand

Genomic View for PLD3 Gene

Genes around PLD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLD3 Gene

Proteins for PLD3 Gene

  • Protein details for PLD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IV08-PLD3_HUMAN
    Recommended name:
    Phospholipase D3
    Protein Accession:
    Q8IV08
    Secondary Accessions:
    • Q92853
    • Q9BW87

    Protein attributes for PLD3 Gene

    Size:
    490 amino acids
    Molecular mass:
    54705 Da
    Quaternary structure:
    • Interacts with APP.
    SequenceCaution:
    • Sequence=AAB16799.1; Type=Frameshift; Positions=52; Evidence={ECO:0000305};

neXtProt entry for PLD3 Gene

Selected DME Specific Peptides for PLD3 Gene

Q8IV08:
  • DTRYNQETPMEICLNGTPALAYLASAPPPLCP
  • YNCSCLA
  • DNHTHSDIQVKLFVVP
  • DIASFYW
  • YIGTSNWSG
  • LHTKFWVVD
  • VRLLISCW
  • KIFEAYW
  • GRTPDLKALL
  • IPYARVNHNKYMVT
  • GSANMDW
  • LARDLTK
  • SAQQGEEVLRQLQTLAP
  • ELPMNEIEAWKAAEKKARWVLLVLILAVVGFGALMTQLFL
  • LVESIPE

Post-translational modifications for PLD3 Gene

Domains & Families for PLD3 Gene

Gene Families for PLD3 Gene

Protein Domains for PLD3 Gene

Graphical View of Domain Structure for InterPro Entry

Q8IV08

UniProtKB/Swiss-Prot:

PLD3_HUMAN :
  • Contains 2 PLD phosphodiesterase domains.
  • Belongs to the phospholipase D family.
Domain:
  • Contains 2 PLD phosphodiesterase domains.
Family:
  • Belongs to the phospholipase D family.
genes like me logo Genes that share domains with PLD3: view

Function for PLD3 Gene

Molecular function for PLD3 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
A phosphatidylcholine + H(2)O = choline + a phosphatidate.
UniProtKB/Swiss-Prot Function:
May be involved in APP processing.

Enzyme Numbers (IUBMB) for PLD3 Gene

Gene Ontology (GO) - Molecular Function for PLD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004630 phospholipase D activity IEA,TAS --
GO:0005515 protein binding IPI 20195357
GO:0016787 hydrolase activity IEA --
GO:0070290 N-acylphosphatidylethanolamine-specific phospholipase D activity IEA --
genes like me logo Genes that share ontologies with PLD3: view
genes like me logo Genes that share phenotypes with PLD3: view

Animal Models for PLD3 Gene

MGI Knock Outs for PLD3:
  • Pld3 tm1e(EUCOMM)Wtsi

Animal Model Products

miRNA for PLD3 Gene

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PLD3 Gene

Localization for PLD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PLD3 Gene

Endoplasmic reticulum membrane; Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PLD3 Gene COMPARTMENTS Subcellular localization image for PLD3 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
plasma membrane 3
cytosol 2
nucleus 2

Gene Ontology (GO) - Cellular Components for PLD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PLD3: view

Pathways & Interactions for PLD3 Gene

genes like me logo Genes that share pathways with PLD3: view

Gene Ontology (GO) - Biological Process for PLD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0016042 lipid catabolic process IEA --
genes like me logo Genes that share ontologies with PLD3: view

No data available for SIGNOR curated interactions for PLD3 Gene

Drugs & Compounds for PLD3 Gene

(3) Drugs for PLD3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Choline Approved Nutra 148
Ethanolamine Experimental Pharma 0

(8) Additional Compounds for PLD3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
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)
PE(P-16:0e/16:0)
  • 2-Hexadecanoyl-1-(1Z-hexadecenyl)-sn-glycero-3-phosphoethanolamine
PEP-16:0/18:1(11Z))
  • 1-(1-Enyl-palmitoyl)-2-vaccenoyl-sn-glycero-3-phosphoethanolamine
  • GPEtn(16:0/18:1)
  • GPEtn(16:0/18:1n7)
  • GPEtn(16:0/18:1w7)
  • GPEtn(34:1)
Phosphatidylcholines Group A
  • (Z,Z)-(1)-(7-Oleoyl-4-oxido-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-enyl)trimethylammonium 4-oxide
  • (Z,Z)-4-hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxo-9-octadecenyl)oxy]-3,5,9-Trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide hydroxide inner salt
  • 1,2-Dioleoyl-rac-glycero-3-phosphocholine
  • 1,2-Dioleoylglycerol-3-phosphorylcholine
  • 1,2-Dioleoylglyceryl-3-phosphorylcholine
68737-67-7
Phosphatidylcholines Group B
  • 1-(1-Enyl-palmitoyl)-2-stearidonoyl-sn-glycero-3-phosphocholine
  • GPCho(16:0/18:4)
  • GPCho(16:0/18:4n3)
  • GPCho(16:0/18:4w3)
  • GPCho(34:4)
88542-95-4
genes like me logo Genes that share compounds with PLD3: view

Transcripts for PLD3 Gene

Unigene Clusters for PLD3 Gene

Phospholipase D family, member 3:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PLD3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d · 4e ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^
SP1: - - - - -
SP2: - - - - - - - -
SP3: - - - - - - - - - -
SP4: - - - - - - -
SP5: - - - - - - - -
SP6: - - - - - - - - -
SP7: - -
SP8: - -
SP9:
SP10: - - - -
SP11: - - -
SP12: - -
SP13: - -
SP14: - - - -
SP15:
SP16: -
SP17: - - -

ExUns: 14a · 14b ^ 15a · 15b · 15c ^ 16 ^ 17 ^ 18a · 18b · 18c
SP1: -
SP2: -
SP3:
SP4: - -
SP5:
SP6:
SP7:
SP8:
SP9: -
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:

Relevant External Links for PLD3 Gene

GeneLoc Exon Structure for
PLD3
ECgene alternative splicing isoforms for
PLD3

Expression for PLD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PLD3 Gene

Protein differential expression in normal tissues from HIPED for PLD3 Gene

This gene is overexpressed in Amniocyte (16.3) and Adrenal (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PLD3 Gene



Protein tissue co-expression partners for PLD3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PLD3 Gene:

PLD3

SOURCE GeneReport for Unigene cluster for PLD3 Gene:

Hs.257008

mRNA Expression by UniProt/SwissProt for PLD3 Gene:

Q8IV08-PLD3_HUMAN
Tissue specificity: Widely expressed. In the brain, high levels of expression are detected in the frontal, temporal and occipital cortices and hippocampus. Expressed at low level in corpus callosum.
genes like me logo Genes that share expression patterns with PLD3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PLD3 Gene

Orthologs for PLD3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PLD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLD3 34 35
  • 99.7 (n)
dog
(Canis familiaris)
Mammalia PLD3 34 35
  • 93.61 (n)
cow
(Bos Taurus)
Mammalia PLD3 34 35
  • 91.97 (n)
rat
(Rattus norvegicus)
Mammalia Pld3 34
  • 88.32 (n)
mouse
(Mus musculus)
Mammalia Pld3 34 16 35
  • 88.18 (n)
oppossum
(Monodelphis domestica)
Mammalia PLD3 35
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PLD3 35
  • 54 (a)
OneToOne
chicken
(Gallus gallus)
Aves PLD3 35
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PLD3 35
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pld3 34
  • 57.63 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC68676 34
zebrafish
(Danio rerio)
Actinopterygii pld3 34 35
  • 63.72 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000199 34
  • 57.48 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG9248 34 35
  • 54.62 (n)
CG43345 35
  • 37 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea F09G2.8 34 35
  • 47.28 (n)
rice
(Oryza sativa)
Liliopsida Os06g0649900 34
  • 41.56 (n)
Species where no ortholog for PLD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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)
  • wheat (Triticum aestivum)

Evolution for PLD3 Gene

ENSEMBL:
Gene Tree for PLD3 (if available)
TreeFam:
Gene Tree for PLD3 (if available)

Paralogs for PLD3 Gene

Paralogs for PLD3 Gene

genes like me logo Genes that share paralogs with PLD3: view

Variants for PLD3 Gene

Sequence variations from dbSNP and Humsavar for PLD3 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs145999145 Uncertain significance 40,371,688(+) TGGGC(A/G)TGGTC reference, missense
rs10407447 -- 40,363,275(+) AAGAC(A/G)AGCAT intron-variant
rs10407665 -- 40,355,915(+) GCTTA(A/G)ATTTC intron-variant
rs10407684 -- 40,355,936(+) ATTTA(A/G)AAGTG intron-variant
rs10407876 -- 40,355,987(+) TTTCA(A/G)ACTGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PLD3 Gene

Variant ID Type Subtype PubMed ID
esv1638921 CNV insertion 17803354
esv2665673 CNV deletion 23128226
esv3644346 CNV loss 21293372
nsv476934 CNV novel sequence insertion 20440878
nsv833831 CNV loss 17160897

Variation tolerance for PLD3 Gene

Residual Variation Intolerance Score: 33% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.39; 27.41% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PLD3 Gene

Human Gene Mutation Database (HGMD)
PLD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLD3 Gene

Disorders for PLD3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for PLD3 Gene - From: OMIM, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
alzheimer disease 19, late onset
  • alzheimer's disease 19
acute conjunctivitis
acute hemorrhagic conjunctivitis
  • apollo disease
conjunctival folliculosis
  • acute follicular conjunctivitis
shipyard eye
  • ekc
- elite association - COSMIC cancer census association via MalaCards
Search PLD3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PLD3_HUMAN
  • Note=Genetic variants in PLD3 have been suggested to be associated with an increased risk for Alzheimer disease (PubMed:24336208, PubMed:25832409). Further studies, however, did not support PLD3 involvement in this disease (PubMed:25832408, PubMed:25832411, PubMed:25832413, PubMed:25832410, PubMed:26411346). {ECO:0000269 PubMed:24336208, ECO:0000269 PubMed:25832408, ECO:0000269 PubMed:25832409, ECO:0000269 PubMed:25832410, ECO:0000269 PubMed:25832411, ECO:0000269 PubMed:25832413, ECO:0000269 PubMed:26411346}.

Relevant External Links for PLD3

Genetic Association Database (GAD)
PLD3
Human Genome Epidemiology (HuGE) Navigator
PLD3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PLD3
genes like me logo Genes that share disorders with PLD3: view

No data available for Genatlas for PLD3 Gene

Publications for PLD3 Gene

  1. Hu-K4 is a ubiquitously expressed type 2 transmembrane protein associated with the endoplasmic reticulum. (PMID: 15794758) Munck A. … Hampe W. (FEBS J. 2005) 2 3 4 22 64
  2. A human homolog of the vaccinia virus HindIII K4L gene is a member of the phospholipase D superfamily. (PMID: 9140189) Cao J.X. … Upton C. (Virus Res. 1997) 2 3 4 64
  3. Rare variants in PLD3 do not affect risk for early-onset Alzheimer disease in a European consortium cohort. (PMID: 26411346) Cacace R. … Van Broeckhoven C. (Hum. Mutat. 2015) 3 4 64
  4. Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer's disease. (PMID: 24336208) Cruchaga C. … Goate A.M. (Nature 2014) 3 4 64
  5. [Over-expression of phospholipase D3 inhibits Akt phosphorylation in C2C12 myoblasts]. (PMID: 20112697) Zhang J. … Wang H. (Sheng Wu Gong Cheng Xue Bao 2009) 3 22 64

Products for PLD3 Gene