Atlas of Genetics and Cytogenetics in Oncology and Haematology


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PKD2 (polycystic kidney disease 2 (autosomal dominant))

Identity

Other namesAPKD2
PC2
PKD4
Pc-2
TRPP2
HGNC (Hugo) PKD2
LocusID (NCBI) 5311
Atlas_Id 41726
Location 4q22.1
Location_base_pair Starts at 88928799 and ends at 88998931 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2015)
TSPAN5 4q23 / PKD2 4q22.1

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

 


External links

Nomenclature
HGNC (Hugo)PKD2   9009
Cards
Entrez_Gene (NCBI)PKD2  5311  polycystic kidney disease 2 (autosomal dominant)
GeneCards (Weizmann)PKD2
Ensembl hg19 (Hinxton)ENSG00000118762 [Gene_View]  chr4:88928799-88998931 [Contig_View]  PKD2 [Vega]
Ensembl hg38 (Hinxton)ENSG00000118762 [Gene_View]  chr4:88928799-88998931 [Contig_View]  PKD2 [Vega]
ICGC DataPortalENSG00000118762
TCGA cBioPortalPKD2
AceView (NCBI)PKD2
Genatlas (Paris)PKD2
WikiGenes5311
SOURCE (Princeton)PKD2
Genomic and cartography
GoldenPath hg19 (UCSC)PKD2  -     chr4:88928799-88998931 +  4q22.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PKD2  -     4q22.1   [Description]    (hg38-Dec_2013)
EnsemblPKD2 - 4q22.1 [CytoView hg19]  PKD2 - 4q22.1 [CytoView hg38]
Mapping of homologs : NCBIPKD2 [Mapview hg19]  PKD2 [Mapview hg38]
OMIM173910   613095   
Gene and transcription
Genbank (Entrez)AF054992 AF113693 AK293461 AK294173 AK294589
RefSeq transcript (Entrez)NM_000297
RefSeq genomic (Entrez)NC_000004 NC_018915 NG_008604 NT_016354 NW_004929320
Consensus coding sequences : CCDS (NCBI)PKD2
Cluster EST : UnigeneHs.181272 [ NCBI ]
CGAP (NCI)Hs.181272
Alternative Splicing : Fast-db (Paris)GSHG0022721
Alternative Splicing GalleryENSG00000118762
Gene ExpressionPKD2 [ NCBI-GEO ]     PKD2 [ SEEK ]   PKD2 [ MEM ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)5311
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13563 (Uniprot)
NextProtQ13563  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ13563
Splice isoforms : SwissVarQ13563 (Swissvar)
PhosPhoSitePlusQ13563
Domaine pattern : Prosite (Expaxy)EF_HAND_2 (PS50222)   
Domains : Interpro (EBI)Channel_four-helix_dom    EF-hand-dom_pair    EF_hand_dom    PKD1_2_channel    PKD_2   
Domain families : Pfam (Sanger)PKD_channel (PF08016)   
Domain families : Pfam (NCBI)pfam08016   
DMDM Disease mutations5311
Blocks (Seattle)PKD2
PDB (SRS)2KLD    2KLE    2KQ6    2Y4Q    3HRN    3HRO   
PDB (PDBSum)2KLD    2KLE    2KQ6    2Y4Q    3HRN    3HRO   
PDB (IMB)2KLD    2KLE    2KQ6    2Y4Q    3HRN    3HRO   
PDB (RSDB)2KLD    2KLE    2KQ6    2Y4Q    3HRN    3HRO   
Structural Biology KnowledgeBase2KLD    2KLE    2KQ6    2Y4Q    3HRN    3HRO   
SCOP (Structural Classification of Proteins)2KLD    2KLE    2KQ6    2Y4Q    3HRN    3HRO   
CATH (Classification of proteins structures)2KLD    2KLE    2KQ6    2Y4Q    3HRN    3HRO   
Human Protein AtlasENSG00000118762
Peptide AtlasQ13563
HPRD01437
IPIIPI00299040   IPI00964610   
Protein Interaction databases
DIP (DOE-UCLA)Q13563
IntAct (EBI)Q13563
FunCoupENSG00000118762
BioGRIDPKD2
IntegromeDBPKD2
STRING (EMBL)PKD2
ZODIACPKD2
Ontologies - Pathways
QuickGOQ13563
Ontology : AmiGObranching involved in ureteric bud morphogenesis  liver development  embryonic placenta development  heart looping  polycystin complex  detection of nodal flow  receptor binding  voltage-gated ion channel activity  voltage-gated calcium channel activity  voltage-gated sodium channel activity  potassium channel activity  calcium ion binding  protein binding  cytoplasm  cytoplasm  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum membrane  cytosol  plasma membrane  integral component of plasma membrane  cell-cell junction  cilium  calcium ion transport  calcium ion transport  cell cycle arrest  JAK-STAT cascade  determination of left/right symmetry  heart development  cytoskeletal protein binding  negative regulation of cell proliferation  basal plasma membrane  spinal cord development  neural tube development  voltage-gated cation channel activity  lamellipodium  regulation of cAMP metabolic process  motile primary cilium  nonmotile primary cilium  positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity  positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle  filamentous actin  cellular response to reactive oxygen species  metanephric part of ureteric bud development  sodium ion transmembrane transport  aorta development  ciliary basal body  regulation of cell proliferation  identical protein binding  identical protein binding  protein homodimerization activity  actinin binding  cytoplasmic sequestering of transcription factor  HLH domain binding  ion channel binding  basal cortex  positive regulation of nitric oxide biosynthetic process  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  calcium-induced calcium release activity  detection of mechanical stimulus  detection of mechanical stimulus  ATPase binding  release of sequestered calcium ion into cytosol  release of sequestered calcium ion into cytosol  phosphoprotein binding  centrosome duplication  muscle alpha-actinin binding  ciliary membrane  negative regulation of ryanodine-sensitive calcium-release channel activity  placenta blood vessel development  renal tubule morphogenesis  renal artery morphogenesis  extracellular exosome  calcium ion transmembrane transport  positive regulation of cell cycle arrest  integral component of cytoplasmic side of endoplasmic reticulum membrane  cellular response to hydrostatic pressure  cellular response to osmotic stress  cellular response to fluid shear stress  integral component of lumenal side of endoplasmic reticulum membrane  potassium ion transmembrane transport  determination of liver left/right asymmetry  metanephric mesenchyme development  mesonephric tubule development  mesonephric duct development  metanephric smooth muscle tissue development  metanephric cortex development  metanephric ascending thin limb development  metanephric cortical collecting duct development  metanephric distal tubule development  metanephric S-shaped body morphogenesis  mitotic spindle  regulation of calcium ion import  negative regulation of G1/S transition of mitotic cell cycle  
Ontology : EGO-EBIbranching involved in ureteric bud morphogenesis  liver development  embryonic placenta development  heart looping  polycystin complex  detection of nodal flow  receptor binding  voltage-gated ion channel activity  voltage-gated calcium channel activity  voltage-gated sodium channel activity  potassium channel activity  calcium ion binding  protein binding  cytoplasm  cytoplasm  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum membrane  cytosol  plasma membrane  integral component of plasma membrane  cell-cell junction  cilium  calcium ion transport  calcium ion transport  cell cycle arrest  JAK-STAT cascade  determination of left/right symmetry  heart development  cytoskeletal protein binding  negative regulation of cell proliferation  basal plasma membrane  spinal cord development  neural tube development  voltage-gated cation channel activity  lamellipodium  regulation of cAMP metabolic process  motile primary cilium  nonmotile primary cilium  positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity  positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle  filamentous actin  cellular response to reactive oxygen species  metanephric part of ureteric bud development  sodium ion transmembrane transport  aorta development  ciliary basal body  regulation of cell proliferation  identical protein binding  identical protein binding  protein homodimerization activity  actinin binding  cytoplasmic sequestering of transcription factor  HLH domain binding  ion channel binding  basal cortex  positive regulation of nitric oxide biosynthetic process  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  calcium-induced calcium release activity  detection of mechanical stimulus  detection of mechanical stimulus  ATPase binding  release of sequestered calcium ion into cytosol  release of sequestered calcium ion into cytosol  phosphoprotein binding  centrosome duplication  muscle alpha-actinin binding  ciliary membrane  negative regulation of ryanodine-sensitive calcium-release channel activity  placenta blood vessel development  renal tubule morphogenesis  renal artery morphogenesis  extracellular exosome  calcium ion transmembrane transport  positive regulation of cell cycle arrest  integral component of cytoplasmic side of endoplasmic reticulum membrane  cellular response to hydrostatic pressure  cellular response to osmotic stress  cellular response to fluid shear stress  integral component of lumenal side of endoplasmic reticulum membrane  potassium ion transmembrane transport  determination of liver left/right asymmetry  metanephric mesenchyme development  mesonephric tubule development  mesonephric duct development  metanephric smooth muscle tissue development  metanephric cortex development  metanephric ascending thin limb development  metanephric cortical collecting duct development  metanephric distal tubule development  metanephric S-shaped body morphogenesis  mitotic spindle  regulation of calcium ion import  negative regulation of G1/S transition of mitotic cell cycle  
Protein Interaction DatabasePKD2
Atlas of Cancer Signalling NetworkPKD2
Wikipedia pathwaysPKD2
Orthology - Evolution
OrthoDB5311
GeneTree (enSembl)ENSG00000118762
Phylogenetic Trees/Animal Genes : TreeFamPKD2
Homologs : HomoloGenePKD2
Homology/Alignments : Family Browser (UCSC)PKD2
Gene fusions - Rearrangements
Fusion: TCGATSPAN5 4q23 PKD2 4q22.1 BRCA
Polymorphisms : SNP, variants
NCBI Variation ViewerPKD2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PKD2
dbVarPKD2
ClinVarPKD2
1000_GenomesPKD2 
Exome Variant ServerPKD2
Exome Aggregation Consortium (ExAC)ENSG00000118762
SNP (GeneSNP Utah)PKD2
SNP : HGBasePKD2
Genetic variants : HAPMAPPKD2
Genomic Variants (DGV)PKD2 [DGVbeta]
Mutations
ICGC Data PortalPKD2 
TCGA Data PortalPKD2 
Tumor PortalPKD2
TCGA Copy Number PortalPKD2
Somatic Mutations in Cancer : COSMICPKD2 
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
LOVD (Leiden Open Variation Database)Autosomal Dominant Polycystic Kidney Disease (ADPKD)
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
BioMutasearch PKD2
DgiDB (Drug Gene Interaction Database)PKD2
DoCM (Curated mutations)PKD2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PKD2 (select a term)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)4:88928799-88998931
CONAN: Copy Number AnalysisPKD2 
Mutations and Diseases : HGMDPKD2
OMIM173910    613095   
MedgenPKD2
NextProtQ13563 [Medical]
TSGene5311
GENETestsPKD2
Huge Navigator PKD2 [HugePedia]  PKD2 [HugeCancerGEM]
snp3D : Map Gene to Disease5311
BioCentury BCIQPKD2
General knowledge
Chemical/Protein Interactions : CTD5311
Chemical/Pharm GKB GenePA33343
Clinical trialPKD2
Other databases
Probes
Litterature
PubMed161 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePKD2
GoPubMedPKD2
iHOPPKD2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Jan 16 19:15:28 CET 2016

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