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Aliases for PLCD1 Gene

Aliases for PLCD1 Gene

  • Phospholipase C Delta 1 2 3 5
  • 1-Phosphatidylinositol 4,5-Bisphosphate Phosphodiesterase Delta-1 2 3
  • Phosphoinositide Phospholipase C-Delta-1 3 4
  • Phospholipase C-III 3 4
  • PLC-Delta-1 3 4
  • EC 3.1.4.11 4 58
  • PLC-III 3 4
  • Phospholipase C, Delta 1 2
  • Phospholipase C-Delta-1 4
  • NDNC3 3

External Ids for PLCD1 Gene

Previous GeneCards Identifiers for PLCD1 Gene

  • GC03M037350
  • GC03U900338
  • GC03M038009

Summaries for PLCD1 Gene

Entrez Gene Summary for PLCD1 Gene

  • This gene encodes a member of the phospholipase C family. Phospholipase C isozymes play critical roles in intracellular signal transduction by catalyzing the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) into the second messengers diacylglycerol (DAG) and inositol triphosphate (IP3). The encoded protein functions as a tumor suppressor in several types of cancer, and mutations in this gene are a cause of hereditary leukonychia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

GeneCards Summary for PLCD1 Gene

PLCD1 (Phospholipase C Delta 1) is a Protein Coding gene. Diseases associated with PLCD1 include Nail Disorder, Nonsyndromic Congenital, 3, and Leukonychia Totalis. Among its related pathways are Calcium signaling pathway and Phospholipase-C Pathway. GO annotations related to this gene include calcium ion binding and phosphoric diester hydrolase activity. An important paralog of this gene is PLCD3.

UniProtKB/Swiss-Prot for PLCD1 Gene

  • The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. Essential for trophoblast and placental development.

Tocris Summary for PLCD1 Gene

  • Phospholipases are a group of enzymes that hydrolyze phospholipids into fatty acids and other lipophilic molecules. There are four major classes; phospholipase A, phospholipase B, phosphoinositide-specific phospholipase C and phospholipase D.

Gene Wiki entry for PLCD1 Gene

Additional gene information for PLCD1 Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PLCD1 Gene

Genomics for PLCD1 Gene

Regulatory Elements for PLCD1 Gene

Enhancers for PLCD1 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
GH03H038028 1.6 FANTOM5 Ensembl ENCODE dbSUPER 10 -0.4 -438 4 BCOR MAX ZMYM3 POLR2A EGR1 FOS RCOR1 CHD2 SMARCA5 MAZ PLCD1 DLEC1
GH03H038147 1.6 FANTOM5 Ensembl ENCODE dbSUPER 4.3 -119.2 -119156 2 HDAC1 ZNF766 GATA2 ATF7 CREM IKZF2 ZEB2 MEF2D MTA1 SMARCA4 SLC22A13 VILL MYD88 PLCD1 OXSR1
GH03H038163 2 FANTOM5 Ensembl ENCODE dbSUPER 3 -137.4 -137437 7 HDGF PKNOX1 MLX ARNT ZFP64 SIN3A FEZF1 DMAP1 ZNF2 YY1 OXSR1 ACAA1 MYD88 C3orf35 GORASP1 SLC22A13 ACVR2B-AS1 VILL PLCD1 DLEC1
GH03H038037 1 ENCODE dbSUPER 5.9 -9.5 -9478 2 HDAC1 CTCF MXI1 ETV1 MAX SIN3A BMI1 ZBTB40 BATF RAD21 DLEC1 PLCD1 PPP2R2DP1
GH03H038102 0.8 FANTOM5 Ensembl 6.2 -72.7 -72691 0 HDAC2 KDM1A MYD88 VILL ACAA1 SLC22A13 PLCD1 OXSR1 SLC22A14 PIR60395 GC03M038048
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PLCD1 on UCSC Golden Path with GeneCards custom track

Promoters for PLCD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000150962 262 1001 BCOR SMARCA5 REST POLR2A EGR1 KLF16 KDM1A RCOR1 ZBTB33

Genomic Location for PLCD1 Gene

Chromosome:
3
Start:
38,007,496 bp from pter
End:
38,029,762 bp from pter
Size:
22,267 bases
Orientation:
Minus strand

Genomic View for PLCD1 Gene

Genes around PLCD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PLCD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PLCD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PLCD1 Gene

Proteins for PLCD1 Gene

  • Protein details for PLCD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P51178-PLCD1_HUMAN
    Recommended name:
    1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1
    Protein Accession:
    P51178
    Secondary Accessions:
    • B3KR14
    • Q86VN8

    Protein attributes for PLCD1 Gene

    Size:
    756 amino acids
    Molecular mass:
    85665 Da
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PLCD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PLCD1 Gene

Selected DME Specific Peptides for PLCD1 Gene

P51178:
  • KGCRCLE
  • CGYVLKP
  • SSTEAYIR
  • SSHNTYL
  • VALNFQT
  • KADKNKD
  • YPVILSLE
  • YHGYTFTSK
  • YAFKASPYP

Post-translational modifications for PLCD1 Gene

  • Glycosylation at posLast=191191 and Thr193
  • Modification sites at PhosphoSitePlus

Other Protein References for PLCD1 Gene

Domains & Families for PLCD1 Gene

Gene Families for PLCD1 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PLCD1: view

No data available for UniProtKB/Swiss-Prot for PLCD1 Gene

Function for PLCD1 Gene

Molecular function for PLCD1 Gene

GENATLAS Biochemistry:
phospholipase C,delta 1,involved in signal transduction
UniProtKB/Swiss-Prot CatalyticActivity:
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1D-myo-inositol 1,4,5-trisphosphate + diacylglycerol.
UniProtKB/Swiss-Prot Function:
The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. Essential for trophoblast and placental development.

Enzyme Numbers (IUBMB) for PLCD1 Gene

Phenotypes From GWAS Catalog for PLCD1 Gene

Gene Ontology (GO) - Molecular Function for PLCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001786 phosphatidylserine binding IEA --
GO:0004435 phosphatidylinositol phospholipase C activity TAS --
GO:0004629 phospholipase C activity IEA --
GO:0004871 signal transducer activity IEA --
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PLCD1: view
genes like me logo Genes that share phenotypes with PLCD1: view

Human Phenotype Ontology for PLCD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PLCD1 Gene

MGI Knock Outs for PLCD1:

Animal Model Products

  • Taconic Biosciences Mouse Models for PLCD1

CRISPR Products

miRNA for PLCD1 Gene

miRTarBase miRNAs that target PLCD1

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PLCD1
  • Applied Biological Materials Clones for PLCD1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Transcription Factor Targets and HOMER Transcription for PLCD1 Gene

Localization for PLCD1 Gene

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 PLCD1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytosol 4
cytoskeleton 3
nucleus 2
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PLCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 15702972
GO:0005829 cytosol IEA --
GO:0005886 plasma membrane TAS --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PLCD1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PLCD1 Gene

Pathways & Interactions for PLCD1 Gene

genes like me logo Genes that share pathways with PLCD1: view

Gene Ontology (GO) - Biological Process for PLCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IEA --
GO:0006629 lipid metabolic process IEA --
GO:0006644 phospholipid metabolic process TAS 9588182
GO:0007165 signal transduction IEA --
GO:0016042 lipid catabolic process IEA --
genes like me logo Genes that share ontologies with PLCD1: view

No data available for SIGNOR curated interactions for PLCD1 Gene

Drugs & Compounds for PLCD1 Gene

(10) Drugs for PLCD1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
1D-myo-inositol 1,4,5-trisphosphate Experimental Pharma Target 0
Inositol 2,4,5-trisphosphate Experimental Pharma Target 0
calcium Nutra 0

(395) Additional Compounds for PLCD1 Gene - From: HMDB, Novoseek, and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Diglycerides Group A
  • 1,2-Dimyristoyl-rac-glycerol
  • DAG(14:0/14:0)
  • DAG(28:0)
  • DG(14:0/14:0)
  • DG(28:0)
Diglycerides Group B
  • 1-Palmitoleoyl-2-arachidonyl-sn-glycerol
  • DAG(16:1/20:0)
  • DAG(16:1n7/20:0)
  • DAG(16:1w7/20:0)
  • DAG(36:1)
Diglycerides Group C
  • 1-Myristoyl-3-behenoyl-sn-glycerol
  • 1-Tetradecanoyl-3-docosanoyl-sn-glycerol
  • DAG(14:0/0:0/22:0)
  • DAG(36:0)
  • DG(36:0)
Diglycerides Group D
  • 1,2-Didocosahexaenoyl-rac-glycerol
  • DAG(22:6/22:6)
  • DAG(22:6n3/22:6n3)
  • DAG(22:6w3/22:6w3)
  • DAG(44:12)
Inositol 1,4,5-trisphosphate
  • 1D-Myo-Inositol 1,4,5-trisphosphate
  • D-Myo-Inositol 1,4,5-trisphosphate
  • Inositol 1,4,5-trisphosphate
88269-39-0

(2) Tocris Compounds for PLCD1 Gene

Compound Action Cas Number
o-3M3FBS Inactive analog of m-3M3FBS (Cat. No. 1941) 313981-55-4
U 73122 Phospholipase C inhibitor 112648-68-7
genes like me logo Genes that share compounds with PLCD1: view

Transcripts for PLCD1 Gene

Unigene Clusters for PLCD1 Gene

Phospholipase C, delta 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for PLCD1
  • Applied Biological Materials Clones for PLCD1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for PLCD1 Gene

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

ExUns: 14a · 14b ^ 15a · 15b ^ 16a · 16b ^ 17 ^ 18
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for PLCD1 Gene

GeneLoc Exon Structure for
PLCD1
ECgene alternative splicing isoforms for
PLCD1

Expression for PLCD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PLCD1 Gene

Protein differential expression in normal tissues from HIPED for PLCD1 Gene

This gene is overexpressed in Spinal cord (15.0) and Brain (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PLCD1 Gene



Protein tissue co-expression partners for PLCD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PLCD1 Gene:

PLCD1

SOURCE GeneReport for Unigene cluster for PLCD1 Gene:

Hs.80776

Evidence on tissue expression from TISSUES for PLCD1 Gene

  • Nervous system(4.8)
  • Liver(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PLCD1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • urinary
Organs:
Head and neck:
  • brain
  • eye
  • eyelid
  • face
  • head
Abdomen:
  • kidney
Pelvis:
  • ureter
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • nail
  • toe
  • upper limb
General:
  • skin
genes like me logo Genes that share expression patterns with PLCD1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PLCD1 Gene

Orthologs for PLCD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PLCD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PLCD1 33 34
  • 98.85 (n)
dog
(Canis familiaris)
Mammalia PLCD1 34 33
  • 90.83 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PLCD1 33 34
  • 89.53 (n)
rat
(Rattus norvegicus)
Mammalia Plcd1 33
  • 86.67 (n)
mouse
(Mus musculus)
Mammalia Plcd1 33 16 34
  • 86.44 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PLCD1 34
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves PLCD1 33 34
  • 68.56 (n)
lizard
(Anolis carolinensis)
Reptilia PLCD1 34
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia plcd1 33
  • 66.58 (n)
zebrafish
(Danio rerio)
Actinopterygii plcd1a 34
  • 55 (a)
OneToMany
plcd1b 34
  • 54 (a)
OneToMany
wufj78d10 33
rice
(Oryza sativa)
Liliopsida Os05g0127200 33
  • 47.79 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 39 (a)
OneToMany
Species where no ortholog for PLCD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for PLCD1 Gene

ENSEMBL:
Gene Tree for PLCD1 (if available)
TreeFam:
Gene Tree for PLCD1 (if available)

Paralogs for PLCD1 Gene

Paralogs for PLCD1 Gene

(9) SIMAP similar genes for PLCD1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PLCD1: view

Variants for PLCD1 Gene

Sequence variations from dbSNP and Humsavar for PLCD1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
VAR_066399 Nail disorder, non-syndromic congenital, 3 (NDNC3) [MIM:151600]
VAR_066400 Nail disorder, non-syndromic congenital, 3 (NDNC3) [MIM:151600]
rs375683615 Pathogenic 38,009,108(+) TCCAG(C/T)CGGGT nc-transcript-variant, reference, missense
rs397514470 Pathogenic 38,009,945(-) TGAAC(C/T)GACCA nc-transcript-variant, reference, stop-gained
rs397514471 Pathogenic 38,011,442(-) AGGAG(C/T)GTGAC nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for PLCD1 Gene

Variant ID Type Subtype PubMed ID
esv2759140 CNV loss 17122850
nsv428416 CNV loss 18775914
nsv508911 CNV insertion 20534489
nsv509821 OTHER sequence alteration 20534489
nsv522354 CNV loss 19592680
nsv590094 CNV loss 21841781
nsv590101 CNV loss 21841781
nsv822058 CNV gain 20364138

Variation tolerance for PLCD1 Gene

Residual Variation Intolerance Score: 24.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.17; 75.86% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PLCD1 Gene

Human Gene Mutation Database (HGMD)
PLCD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PLCD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PLCD1 Gene

Disorders for PLCD1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PLCD1 Gene - From: HGMD, OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
nail disorder, nonsyndromic congenital, 3,
  • nonsyndromic congenital nail disorder 3
leukonychia totalis
  • hereditary white nails
bart-pumphrey syndrome
  • knuckle pads, leukonychia, and sensorineural deafness
nail disease
  • abnormality of the nail
corneal fleck dystrophy
  • fleck corneal dystrophy
- elite association - COSMIC cancer census association via MalaCards
Search PLCD1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PLCD1_HUMAN
  • Nail disorder, non-syndromic congenital, 3 (NDNC3) [MIM:151600]: A nail disorder characterized by a white appearance of the nail plate (true leukonychia), the nail bed (pseudoleukonychia), or neither (apparent leukonychia). Leukonychia may involve all of the nail (leukonychia totalis) or only part of the nail (leukonychia partialis), or can appear as one or more transverse bands (leukonychia striata) or white spots (leukonychia punctata). {ECO:0000269 PubMed:21665001}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PLCD1

Genetic Association Database (GAD)
PLCD1
Human Genome Epidemiology (HuGE) Navigator
PLCD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PLCD1
genes like me logo Genes that share disorders with PLCD1: view

No data available for Genatlas for PLCD1 Gene

Publications for PLCD1 Gene

  1. Genomic structure of the human PLCD1 (phospholipase C delta 1) locus on 3p22-->p21.3. (PMID: 9345909) Ishikawa S … Nakamura Y (Cytogenetics and cell genetics 1997) 2 3 22 60
  2. Cloning and identification of amino acid residues of human phospholipase C delta 1 essential for catalysis. (PMID: 7890667) Cheng HF … King K (The Journal of biological chemistry 1995) 3 4 22 60
  3. Hereditary leukonychia, or porcelain nails, resulting from mutations in PLCD1. (PMID: 21665001) Kiuru M … Christiano AM (American journal of human genetics 2011) 3 4 60
  4. Polymorphisms in innate immunity genes and patients response to dendritic cell-based HIV immuno-treatment. (PMID: 20056178) Segat L … Crovella S (Vaccine 2010) 3 45 60
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 45 60

Products for PLCD1 Gene

  • Addgene plasmids for PLCD1

Sources for PLCD1 Gene

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