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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
Donations are also welcome

Donate (in Euros)

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

Identity

Other namesARPKD
FCYT
TIGM1
HGNC (Hugo) PKHD1
LocusID (NCBI) 5314
Location 6p12.3
Location_base_pair Starts at 51480145 and ends at 51952423 bp from pter ( according to hg19-Feb_2009)
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

External links

Nomenclature
HGNC (Hugo)PKHD1   9016
Cards
Entrez_Gene (NCBI)PKHD1  5314  polycystic kidney and hepatic disease 1 (autosomal recessive)
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
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)AC_000138 NC_000006 NC_018917 NG_008753 NT_007592 NW_001838981 NW_004929326
Consensus coding sequences : CCDS (NCBI)PKHD1
Cluster EST : UnigeneHs.662050 [ NCBI ]
CGAP (NCI)Hs.662050
Alternative Splicing : Fast-db (Paris)GSHG0026675
Alternative Splicing GalleryENSG00000170927
Gene ExpressionPKHD1 [ NCBI-GEO ]     PKHD1 [ SEEK ]   PKHD1 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP08F94 (Uniprot)
NextProtP08F94  [Medical]
With graphics : InterProP08F94
Splice isoforms : SwissVarP08F94 (Swissvar)
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   
Related proteins : CluSTrP08F94
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)P08F94
Human Protein AtlasENSG00000170927
Peptide AtlasP08F94
HPRD05987
IPIIPI00293274   IPI00239117   IPI00874155   
Protein Interaction databases
DIP (DOE-UCLA)P08F94
IntAct (EBI)P08F94
FunCoupENSG00000170927
BioGRIDPKHD1
IntegromeDBPKHD1
STRING (EMBL)PKHD1
Ontologies - Pathways
QuickGOP08F94
Ontology : AmiGOkidney 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 vesicular exosome  regulation of ERK1 and ERK2 cascade  primary cilium  mitotic spindle  
Ontology : EGO-EBIkidney 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 vesicular exosome  regulation of ERK1 and ERK2 cascade  primary cilium  mitotic spindle  
Protein Interaction DatabasePKHD1
DoCM (Curated mutations)PKHD1
Wikipedia pathwaysPKHD1
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerPKHD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PKHD1
dbVarPKHD1
ClinVarPKHD1
1000_GenomesPKHD1 
Exome Variant ServerPKHD1
SNP (GeneSNP Utah)PKHD1
SNP : HGBasePKHD1
Genetic variants : HAPMAPPKHD1
Genomic Variants (DGV)PKHD1 [DGVbeta]
Mutations
ICGC Data PortalENSG00000170927 
Somatic Mutations in Cancer : COSMICPKHD1 
CONAN: Copy Number AnalysisPKHD1 
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
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)6:51480145-51952423
Mutations and Diseases : HGMDPKHD1
OMIM263200    606702   
MedgenPKHD1
NextProtP08F94 [Medical]
GENETestsPKHD1
Disease Genetic AssociationPKHD1
Huge Navigator PKHD1 [HugePedia]  PKHD1 [HugeCancerGEM]
snp3D : Map Gene to Disease5314
DGIdb (Drug Gene Interaction db)PKHD1
General knowledge
Homologs : HomoloGenePKHD1
Homology/Alignments : Family Browser (UCSC)PKHD1
Phylogenetic Trees/Animal Genes : TreeFamPKHD1
Chemical/Protein Interactions : CTD5314
Chemical/Pharm GKB GenePA33348
Clinical trialPKHD1
Cancer Resource (Charite)ENSG00000170927
Other databases
Probes
Litterature
PubMed50 Pubmed reference(s) in Entrez
CoreMinePKHD1
GoPubMedPKHD1
iHOPPKHD1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated12-2014Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Feb 14 18:00:26 CET 2015

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