Atlas of Genetics and Cytogenetics in Oncology and Haematology

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PKHD1 (polycystic kidney and hepatic disease 1 (autosomal recessive))

Identity

Other namesARPKD
FCYT
TIGM1
HGNC (Hugo) PKHD1
LocusID (NCBI) 5314
Atlas_Id 52174
Location 6p12.3  [Link to chromosome band 6p12]
Location_base_pair Starts at 51480145 and ends at 51952423 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)		DHRS7B (17p11.2) / PKHD1 (6p12.3)PKHD1 (6p12.3) / RCAN2 (6p21.1)PKHD1 6p12.3 / RCAN2 6p21.1

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)PKHD1   9016
Cards
Entrez_Gene (NCBI)PKHD1  5314  polycystic kidney and hepatic disease 1 (autosomal recessive)
AliasesARPKD; FCYT; TIGM1
GeneCards (Weizmann)PKHD1
Ensembl hg19 (Hinxton)ENSG00000170927 [Gene_View]  chr6:51480145-51952423 [Contig_View]  PKHD1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000170927 [Gene_View]  chr6:51480145-51952423 [Contig_View]  PKHD1 [Vega]
ICGC DataPortalENSG00000170927
TCGA cBioPortalPKHD1
AceView (NCBI)PKHD1
Genatlas (Paris)PKHD1
WikiGenes5314
SOURCE (Princeton)PKHD1
Genomic and cartography
GoldenPath hg19 (UCSC)PKHD1  -     chr6:51480145-51952423 -  6p12.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PKHD1  -     6p12.3   [Description]    (hg38-Dec_2013)
EnsemblPKHD1 - 6p12.3 [CytoView hg19]  PKHD1 - 6p12.3 [CytoView hg38]
Mapping of homologs : NCBIPKHD1 [Mapview hg19]  PKHD1 [Mapview hg38]
OMIM263200   606702   
Gene and transcription
Genbank (Entrez)AF480064 AK091971 AK128031 AY074797 AY092083
RefSeq transcript (Entrez)NM_138694 NM_170724
RefSeq genomic (Entrez)NC_000006 NC_018917 NG_008753 NT_007592 NW_004929326
Consensus coding sequences : CCDS (NCBI)PKHD1
Cluster EST : UnigeneHs.662050 [ NCBI ]
CGAP (NCI)Hs.662050
Alternative Splicing GalleryENSG00000170927
Gene ExpressionPKHD1 [ NCBI-GEO ]   PKHD1 [ EBI - ARRAY_EXPRESS ]   PKHD1 [ SEEK ]   PKHD1 [ MEM ]
Gene Expression Viewer (FireBrowse)PKHD1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5314
GTEX Portal (Tissue expression)PKHD1
Protein : pattern, domain, 3D structure
UniProt/SwissProtP08F94 (Uniprot)
NextProtP08F94  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP08F94
Splice isoforms : SwissVarP08F94 (Swissvar)
PhosPhoSitePlusP08F94
Domaine pattern : Prosite (Expaxy)G8 (PS51484)   
Domains : Interpro (EBI)G8_domain    Ig-like_fold    Ig_E-set    IPT    PbH1    Pectin_lyas_fold    Pectin_lyase_fold/virulence    PKHD1   
Domain families : Pfam (Sanger)G8 (PF10162)    TIG (PF01833)   
Domain families : Pfam (NCBI)pfam10162    pfam01833   
Domain families : Smart (EMBL)IPT (SM00429)  PbH1 (SM00710)  
DMDM Disease mutations5314
Blocks (Seattle)PKHD1
SuperfamilyP08F94
Human Protein AtlasENSG00000170927
Peptide AtlasP08F94
HPRD05987
IPIIPI00293274   IPI00239117   IPI00874155   
Protein Interaction databases
DIP (DOE-UCLA)P08F94
IntAct (EBI)P08F94
FunCoupENSG00000170927
BioGRIDPKHD1
STRING (EMBL)PKHD1
ZODIACPKHD1
Ontologies - Pathways
QuickGOP08F94
Ontology : AmiGOchromosome, centromeric region  kidney development  receptor activity  protein binding  cytoplasm  centrosome  cellular calcium ion homeostasis  positive regulation of cell proliferation  regulation of centrosome duplication  integral component of membrane  apical plasma membrane  single organismal cell-cell adhesion  anchored component of external side of plasma membrane  regulation of TOR signaling  negative regulation of NF-kappaB transcription factor activity  ciliary basal body  cilium assembly  homeostatic process  negative regulation of apoptotic process  perinuclear region of cytoplasm  negative regulation of cellular component movement  negative regulation of protein kinase B signaling  extracellular exosome  regulation of ERK1 and ERK2 cascade  primary cilium  mitotic spindle  
Ontology : EGO-EBIchromosome, centromeric region  kidney development  receptor activity  protein binding  cytoplasm  centrosome  cellular calcium ion homeostasis  positive regulation of cell proliferation  regulation of centrosome duplication  integral component of membrane  apical plasma membrane  single organismal cell-cell adhesion  anchored component of external side of plasma membrane  regulation of TOR signaling  negative regulation of NF-kappaB transcription factor activity  ciliary basal body  cilium assembly  homeostatic process  negative regulation of apoptotic process  perinuclear region of cytoplasm  negative regulation of cellular component movement  negative regulation of protein kinase B signaling  extracellular exosome  regulation of ERK1 and ERK2 cascade  primary cilium  mitotic spindle  
NDEx NetworkPKHD1
Atlas of Cancer Signalling NetworkPKHD1
Wikipedia pathwaysPKHD1
Orthology - Evolution
OrthoDB5314
GeneTree (enSembl)ENSG00000170927
Phylogenetic Trees/Animal Genes : TreeFamPKHD1
Homologs : HomoloGenePKHD1
Homology/Alignments : Family Browser (UCSC)PKHD1
Gene fusions - Rearrangements
Fusion: TCGAPKHD1 6p12.3 RCAN2 6p21.1 KIRC
Polymorphisms : SNP, variants
NCBI Variation ViewerPKHD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PKHD1
dbVarPKHD1
ClinVarPKHD1
1000_GenomesPKHD1 
Exome Variant ServerPKHD1
ExAC (Exome Aggregation Consortium)PKHD1 (select the gene name)
Genetic variants : HAPMAP5314
Genomic Variants (DGV)PKHD1 [DGVbeta]
Mutations
ICGC Data PortalPKHD1 
TCGA Data PortalPKHD1 
Broad Tumor PortalPKHD1
OASIS PortalPKHD1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPKHD1 
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 PKHD1
DgiDB (Drug Gene Interaction Database)PKHD1
DoCM (Curated mutations)PKHD1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PKHD1 (select a term)
intoGenPKHD1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)6:51480145-51952423  ENSG00000170927
CONAN: Copy Number AnalysisPKHD1 
Mutations and Diseases : HGMDPKHD1
OMIM263200    606702   
MedgenPKHD1
Genetic Testing Registry PKHD1
NextProtP08F94 [Medical]
TSGene5314
GENETestsPKHD1
Huge Navigator PKHD1 [HugePedia]
snp3D : Map Gene to Disease5314
BioCentury BCIQPKHD1
ClinGenPKHD1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5314
Chemical/Pharm GKB GenePA33348
Clinical trialPKHD1
Miscellaneous
canSAR (ICR)PKHD1 (select the gene name)
Probes
Litterature
PubMed60 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePKHD1
EVEXPKHD1
GoPubMedPKHD1
iHOPPKHD1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 19 19:07:16 CEST 2016
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