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GPCPD1 (glycerophosphocholine phosphodiesterase 1)

Identity

Alias_namesglycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)
Alias_symbol (synonym)KIAA1434
GDE5
GDPD6
Other aliasEDI3
PREI4
HGNC (Hugo) GPCPD1
LocusID (NCBI) 56261
Atlas_Id 55316
Location 20p12.3  [Link to chromosome band 20p12]
Location_base_pair Starts at 5544434 and ends at 5611026 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
FSTL1 (3q13.33) / GPCPD1 (20p12.3)GPCPD1 (20p12.3) / CLDND1 (3q11.2)GPCPD1 (20p12.3) / FSTL1 (3q13.33)
PLCB1 (20p12.3) / GPCPD1 (20p12.3)SYTL4 (Xq22.1) / GPCPD1 (20p12.3)PLCB1 20p12.3 / GPCPD1 20p12.3

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  PLCB1/GPCPD1 (20p12)

External links

Nomenclature
HGNC (Hugo)GPCPD1   26957
Cards
Entrez_Gene (NCBI)GPCPD1  56261  glycerophosphocholine phosphodiesterase 1
AliasesEDI3; GDE5; GDPD6; PREI4
GeneCards (Weizmann)GPCPD1
Ensembl hg19 (Hinxton)ENSG00000125772 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000125772 [Gene_View]  ENSG00000125772 [Sequence]  chr20:5544434-5611026 [Contig_View]  GPCPD1 [Vega]
ICGC DataPortalENSG00000125772
TCGA cBioPortalGPCPD1
AceView (NCBI)GPCPD1
Genatlas (Paris)GPCPD1
WikiGenes56261
SOURCE (Princeton)GPCPD1
Genetics Home Reference (NIH)GPCPD1
Genomic and cartography
GoldenPath hg38 (UCSC)GPCPD1  -     chr20:5544434-5611026 -  20p12.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)GPCPD1  -     20p12.3   [Description]    (hg19-Feb_2009)
GoldenPathGPCPD1 - 20p12.3 [CytoView hg19]  GPCPD1 - 20p12.3 [CytoView hg38]
ImmunoBaseENSG00000125772
Mapping of homologs : NCBIGPCPD1 [Mapview hg19]  GPCPD1 [Mapview hg38]
OMIM614124   
Gene and transcription
Genbank (Entrez)AB037855 AK001947 AK308111 AL049446 AL833069
RefSeq transcript (Entrez)NM_019593
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)GPCPD1
Cluster EST : UnigeneHs.636359 [ NCBI ]
CGAP (NCI)Hs.636359
Alternative Splicing GalleryENSG00000125772
Gene ExpressionGPCPD1 [ NCBI-GEO ]   GPCPD1 [ EBI - ARRAY_EXPRESS ]   GPCPD1 [ SEEK ]   GPCPD1 [ MEM ]
Gene Expression Viewer (FireBrowse)GPCPD1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)56261
GTEX Portal (Tissue expression)GPCPD1
Human Protein AtlasENSG00000125772-GPCPD1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NPB8   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NPB8  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NPB8
Splice isoforms : SwissVarQ9NPB8
PhosPhoSitePlusQ9NPB8
Domaine pattern : Prosite (Expaxy)CBM20 (PS51166)    GP_PDE (PS51704)   
Domains : Interpro (EBI)Carb-bd-like_fold    CBM20_GPCPD1    CBM_fam20    Gde1    GP_PDE_dom    Ig-like_fold    PLC-like_Pdiesterase_TIM-brl   
Domain families : Pfam (Sanger)CBM_20 (PF00686)    GDPD (PF03009)   
Domain families : Pfam (NCBI)pfam00686    pfam03009   
Domain families : Smart (EMBL)CBM_2 (SM01065)  
Conserved Domain (NCBI)GPCPD1
DMDM Disease mutations56261
Blocks (Seattle)GPCPD1
PDB (RSDB)2Z0B   
PDB Europe2Z0B   
PDB (PDBSum)2Z0B   
PDB (IMB)2Z0B   
Structural Biology KnowledgeBase2Z0B   
SCOP (Structural Classification of Proteins)2Z0B   
CATH (Classification of proteins structures)2Z0B   
SuperfamilyQ9NPB8
Human Protein Atlas [tissue]ENSG00000125772-GPCPD1 [tissue]
Peptide AtlasQ9NPB8
HPRD10025
IPIIPI00099820   IPI00514636   
Protein Interaction databases
DIP (DOE-UCLA)Q9NPB8
IntAct (EBI)Q9NPB8
FunCoupENSG00000125772
BioGRIDGPCPD1
STRING (EMBL)GPCPD1
ZODIACGPCPD1
Ontologies - Pathways
QuickGOQ9NPB8
Ontology : AmiGOcytosol  skeletal muscle tissue development  glycerophospholipid catabolic process  glycerophosphocholine phosphodiesterase activity  starch binding  
Ontology : EGO-EBIcytosol  skeletal muscle tissue development  glycerophospholipid catabolic process  glycerophosphocholine phosphodiesterase activity  starch binding  
NDEx NetworkGPCPD1
Atlas of Cancer Signalling NetworkGPCPD1
Wikipedia pathwaysGPCPD1
Orthology - Evolution
OrthoDB56261
GeneTree (enSembl)ENSG00000125772
Phylogenetic Trees/Animal Genes : TreeFamGPCPD1
HOGENOMQ9NPB8
Homologs : HomoloGeneGPCPD1
Homology/Alignments : Family Browser (UCSC)GPCPD1
Gene fusions - Rearrangements
Fusion : MitelmanPLCB1/GPCPD1 [20p12.3/20p12.3]  [t(20;20)(p12;p12)]  
Fusion PortalPLCB1 20p12.3 GPCPD1 20p12.3 BRCA
Fusion Cancer (Beijing)GPCPD1 [20p12.3]  -  CLDND1 [3q11.2]  [FUSC000540]
Fusion : QuiverGPCPD1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerGPCPD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)GPCPD1
dbVarGPCPD1
ClinVarGPCPD1
1000_GenomesGPCPD1 
Exome Variant ServerGPCPD1
ExAC (Exome Aggregation Consortium)ENSG00000125772
GNOMAD BrowserENSG00000125772
Varsome BrowserGPCPD1
Genetic variants : HAPMAP56261
Genomic Variants (DGV)GPCPD1 [DGVbeta]
DECIPHERGPCPD1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisGPCPD1 
Mutations
ICGC Data PortalGPCPD1 
TCGA Data PortalGPCPD1 
Broad Tumor PortalGPCPD1
OASIS PortalGPCPD1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICGPCPD1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DGPCPD1
Mutations and Diseases : HGMDGPCPD1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch GPCPD1
DgiDB (Drug Gene Interaction Database)GPCPD1
DoCM (Curated mutations)GPCPD1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)GPCPD1 (select a term)
intoGenGPCPD1
Cancer3DGPCPD1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM614124   
Orphanet
DisGeNETGPCPD1
MedgenGPCPD1
Genetic Testing Registry GPCPD1
NextProtQ9NPB8 [Medical]
TSGene56261
GENETestsGPCPD1
Target ValidationGPCPD1
Huge Navigator GPCPD1 [HugePedia]
snp3D : Map Gene to Disease56261
BioCentury BCIQGPCPD1
ClinGenGPCPD1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD56261
Chemical/Pharm GKB GenePA165392351
Clinical trialGPCPD1
Miscellaneous
canSAR (ICR)GPCPD1 (select the gene name)
DataMed IndexGPCPD1
Probes
Litterature
PubMed12 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineGPCPD1
EVEXGPCPD1
GoPubMedGPCPD1
iHOPGPCPD1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Nov 13 17:45:25 CET 2019
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