Atlas of Genetics and Cytogenetics in Oncology and Haematology

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PKHD1 (PKHD1 ciliary IPT domain containing fibrocystin/polyductin)

Identity

Alias_namesTIGM1
TIG multiple domains 1
Alias_symbol (synonym)ARPKD
FCYT
Other aliasFPC
PKD4
HGNC (Hugo) PKHD1
LocusID (NCBI) 5314
Atlas_Id 52174
Location 6p12.3  [Link to chromosome band 6p12]
Location_base_pair Starts at 51720849 and ends at 52087625 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)
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

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]

Solid Tumors TT_t0606p12p12ID107027 TT_t0606p12p12ID107029

External links

Nomenclature
HGNC (Hugo)PKHD1   9016
Cards
Entrez_Gene (NCBI)PKHD1  5314  PKHD1 ciliary IPT domain containing fibrocystin/polyductin
AliasesARPKD; FCYT; FPC; PKD4; 
TIGM1
GeneCards (Weizmann)PKHD1
Ensembl hg19 (Hinxton)ENSG00000170927 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000170927 [Gene_View]  ENSG00000170927 [Sequence]  chr6:51720849-52087625 [Contig_View]  PKHD1 [Vega]
ICGC DataPortalENSG00000170927
TCGA cBioPortalPKHD1
AceView (NCBI)PKHD1
Genatlas (Paris)PKHD1
WikiGenes5314
SOURCE (Princeton)PKHD1
Genetics Home Reference (NIH)PKHD1
Genomic and cartography
GoldenPath hg38 (UCSC)PKHD1  -     chr6:51720849-52087625 -  6p12.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PKHD1  -     6p12.3   [Description]    (hg19-Feb_2009)
GoldenPathPKHD1 - 6p12.3 [CytoView hg19]  PKHD1 - 6p12.3 [CytoView hg38]
ImmunoBaseENSG00000170927
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)
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]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5314
GTEX Portal (Tissue expression)PKHD1
Human Protein AtlasENSG00000170927-PKHD1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP08F94   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP08F94  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP08F94
Splice isoforms : SwissVarP08F94
PhosPhoSitePlusP08F94
Domaine pattern : Prosite (Expaxy)G8 (PS51484)    PA14 (PS51820)   
Domains : Interpro (EBI)G8_domain    Ig-like_fold    Ig_E-set    IPT_dom    PA14/GLEYA    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)G8 (SM01225)  IPT (SM00429)  PbH1 (SM00710)  
Conserved Domain (NCBI)PKHD1
DMDM Disease mutations5314
Blocks (Seattle)PKHD1
SuperfamilyP08F94
Human Protein Atlas [tissue]ENSG00000170927-PKHD1 [tissue]
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  protein binding  cytoplasm  centrosome  cilium  cilium  cellular calcium ion homeostasis  positive regulation of cell proliferation  regulation of centrosome duplication  integral component of membrane  apical plasma membrane  anchored component of external side of plasma membrane  regulation of TOR signaling  negative regulation of NF-kappaB transcription factor activity  ciliary basal body  signaling receptor activity  homeostatic process  negative regulation of apoptotic process  perinuclear region of cytoplasm  negative regulation of cellular component movement  negative regulation of protein kinase B signaling  cilium assembly  extracellular exosome  regulation of ERK1 and ERK2 cascade  mitotic spindle  cell-cell adhesion  
Ontology : EGO-EBIchromosome, centromeric region  kidney development  protein binding  cytoplasm  centrosome  cilium  cilium  cellular calcium ion homeostasis  positive regulation of cell proliferation  regulation of centrosome duplication  integral component of membrane  apical plasma membrane  anchored component of external side of plasma membrane  regulation of TOR signaling  negative regulation of NF-kappaB transcription factor activity  ciliary basal body  signaling receptor activity  homeostatic process  negative regulation of apoptotic process  perinuclear region of cytoplasm  negative regulation of cellular component movement  negative regulation of protein kinase B signaling  cilium assembly  extracellular exosome  regulation of ERK1 and ERK2 cascade  mitotic spindle  cell-cell adhesion  
NDEx NetworkPKHD1
Atlas of Cancer Signalling NetworkPKHD1
Wikipedia pathwaysPKHD1
Orthology - Evolution
OrthoDB5314
GeneTree (enSembl)ENSG00000170927
Phylogenetic Trees/Animal Genes : TreeFamPKHD1
HOGENOMP08F94
Homologs : HomoloGenePKHD1
Homology/Alignments : Family Browser (UCSC)PKHD1
Gene fusions - Rearrangements
Fusion : MitelmanPKHD1/RCAN2 [6p12.3/6p21.1]  
Fusion PortalPKHD1 6p12.3 RCAN2 6p21.1 KIRC
Fusion : QuiverPKHD1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPKHD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PKHD1
dbVarPKHD1
ClinVarPKHD1
1000_GenomesPKHD1 
Exome Variant ServerPKHD1
ExAC (Exome Aggregation Consortium)ENSG00000170927
GNOMAD BrowserENSG00000170927
Varsome BrowserPKHD1
Genetic variants : HAPMAP5314
Genomic Variants (DGV)PKHD1 [DGVbeta]
DECIPHERPKHD1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPKHD1 
Mutations
ICGC Data PortalPKHD1 
TCGA Data PortalPKHD1 
Broad Tumor PortalPKHD1
OASIS PortalPKHD1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPKHD1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DPKHD1
Mutations and Diseases : HGMDPKHD1
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
Cancer3DPKHD1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM263200    606702   
Orphanet97    10715   
DisGeNETPKHD1
MedgenPKHD1
Genetic Testing Registry PKHD1
NextProtP08F94 [Medical]
TSGene5314
GENETestsPKHD1
Target ValidationPKHD1
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)
DataMed IndexPKHD1
Probes
Litterature
PubMed77 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 Aug 12 15:49:43 CEST 2019
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