Atlas of Genetics and Cytogenetics in Oncology and Haematology

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PRKDC (protein kinase, DNA-activated, catalytic subunit)

Identity

Alias_namesHYRC
HYRC1
protein kinase, DNA-activated, catalytic polypeptide
Alias_symbol (synonym)DNPK1
p350
DNAPK
XRCC7
DNA-PKcs
DNAPKc
DNA-PKC
p460
Other aliasIMD26
HGNC (Hugo) PRKDC
LocusID (NCBI) 5591
Atlas_Id 338
Location 8q11.21  [Link to chromosome band 8q11]
Location_base_pair Starts at 47773108 and ends at 47960183 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)
ACACA (17q12) / PRKDC (8q11.21)DDX5 (17q23.3) / PRKDC (8q11.21)ERC1 (12p13.33) / PRKDC (8q11.21)
KCMF1 (2p11.2) / PRKDC (8q11.21)LOC100507412 (-) / PRKDC (8q11.21)MAP4K5 (14q21.3) / PRKDC (8q11.21)
MCM4 (8q11.21) / PRKDC (8q11.21)MRPS34 (16p13.3) / PRKDC (8q11.21)PRKDC (8q11.21) / ACADVL (17p13.1)
PRKDC (8q11.21) / C8orf22 (8q11.21)PRKDC (8q11.21) / CEP290 (12q21.32)PRKDC (8q11.21) / FAU (11q13.1)
PRKDC (8q11.21) / LAMB1 (7q31.1)PRKDC (8q11.21) / MYO5A (15q21.2)PRKDC (8q11.21) / PRKDC (8q11.21)
PRKDC (8q11.21) / SLC38A2 (12q13.11)PRKDC (8q11.21) / SVIL (10p11.23)PRKDC (8q11.21) / UBE2V2 (8q11.21)
PRKDC (8q11.21) / WDR83 (19p13.2)RPRD1A (18q12.2) / PRKDC (8q11.21)RREB1 (6p24.3) / PRKDC (8q11.21)
SLC39A14 (8p21.3) / PRKDC (8q11.21)SYN3 (22q12.3) / PRKDC (8q11.21)VASH1 (14q24.3) / PRKDC (8q11.21)
KCMF1 2p11.2 / PRKDC 8q11.21PRKDC 8q11.21 / CEP290 12q21.32PRKDC 8q11.21 / MYO5A 15q21.2
PRKDC 8q11.21 / UBE2V2 8q11.21SLC39A14 8p21.3 / PRKDC 8q11.21

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) [ 8 ]
  Lung: Translocations in Squamous Cell Carcinoma
t(2;8)(p11;q11) KCMF1/PRKDC
t(8;8)(p21;q11) SLC39A14/PRKDC
PRKDC/UBE2V2 (8q11)
PRKDC/C8orf22 (8q11)
t(8;8)(q11;q22) CPQ/PRKDC
t(8;12)(q11;q21) PRKDC/CEP290
t(8;15)(q11;q21) PRKDC/MYO5A

External links

Nomenclature
HGNC (Hugo)PRKDC   9413
LRG (Locus Reference Genomic)LRG_162
Cards
Entrez_Gene (NCBI)PRKDC  5591  protein kinase, DNA-activated, catalytic subunit
AliasesDNA-PKC; DNA-PKcs; DNAPK; DNAPKc; 
DNPK1; HYRC; HYRC1; IMD26; XRCC7; p350
GeneCards (Weizmann)PRKDC
Ensembl hg19 (Hinxton)ENSG00000253729 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000253729 [Gene_View]  ENSG00000253729 [Sequence]  chr8:47773108-47960183 [Contig_View]  PRKDC [Vega]
ICGC DataPortalENSG00000253729
TCGA cBioPortalPRKDC
AceView (NCBI)PRKDC
Genatlas (Paris)PRKDC
WikiGenes5591
SOURCE (Princeton)PRKDC
Genetics Home Reference (NIH)PRKDC
Genomic and cartography
GoldenPath hg38 (UCSC)PRKDC  -     chr8:47773108-47960183 -  8q11.21   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PRKDC  -     8q11.21   [Description]    (hg19-Feb_2009)
GoldenPathPRKDC - 8q11.21 [CytoView hg19]  PRKDC - 8q11.21 [CytoView hg38]
ImmunoBaseENSG00000253729
Mapping of homologs : NCBIPRKDC [Mapview hg19]  PRKDC [Mapview hg38]
OMIM600899   615966   
Gene and transcription
Genbank (Entrez)AB208860 AK296833 BC017494 BC024963 BC037968
RefSeq transcript (Entrez)NM_001081640 NM_006904
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PRKDC
Cluster EST : UnigeneHs.491682 [ NCBI ]
CGAP (NCI)Hs.491682
Alternative Splicing GalleryENSG00000253729
Gene ExpressionPRKDC [ NCBI-GEO ]   PRKDC [ EBI - ARRAY_EXPRESS ]   PRKDC [ SEEK ]   PRKDC [ MEM ]
Gene Expression Viewer (FireBrowse)PRKDC [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5591
GTEX Portal (Tissue expression)PRKDC
Human Protein AtlasENSG00000253729-PRKDC [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP78527   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP78527  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP78527
Splice isoforms : SwissVarP78527
Catalytic activity : Enzyme2.7.11.1 [ Enzyme-Expasy ]   2.7.11.12.7.11.1 [ IntEnz-EBI ]   2.7.11.1 [ BRENDA ]   2.7.11.1 [ KEGG ]   
PhosPhoSitePlusP78527
Domaine pattern : Prosite (Expaxy)FAT (PS51189)    FATC (PS51190)    PI3_4_KINASE_1 (PS00915)    PI3_4_KINASE_2 (PS00916)    PI3_4_KINASE_3 (PS50290)   
Domains : Interpro (EBI)ARM-type_fold    DNA-PK_dom    FATC_dom    Kinase-like_dom_sf    NUC194    PI3/4_kinase_cat_dom    PI3/4_kinase_cat_sf    PI3/4_kinase_CS    PIK-rel_kinase_FAT    PIK_FAT   
Domain families : Pfam (Sanger)FAT (PF02259)    FATC (PF02260)    NUC194 (PF08163)    PI3_PI4_kinase (PF00454)   
Domain families : Pfam (NCBI)pfam02259    pfam02260    pfam08163    pfam00454   
Domain families : Smart (EMBL)FATC (SM01343)  NUC194 (SM01344)  PI3Kc (SM00146)  
Conserved Domain (NCBI)PRKDC
DMDM Disease mutations5591
Blocks (Seattle)PRKDC
PDB (RSDB)5LUQ    5W1R    5Y3R   
PDB Europe5LUQ    5W1R    5Y3R   
PDB (PDBSum)5LUQ    5W1R    5Y3R   
PDB (IMB)5LUQ    5W1R    5Y3R   
Structural Biology KnowledgeBase5LUQ    5W1R    5Y3R   
SCOP (Structural Classification of Proteins)5LUQ    5W1R    5Y3R   
CATH (Classification of proteins structures)5LUQ    5W1R    5Y3R   
SuperfamilyP78527
Human Protein Atlas [tissue]ENSG00000253729-PRKDC [tissue]
Peptide AtlasP78527
HPRD02941
IPIIPI00296337   IPI00376215   
Protein Interaction databases
DIP (DOE-UCLA)P78527
IntAct (EBI)P78527
FunCoupENSG00000253729
BioGRIDPRKDC
STRING (EMBL)PRKDC
ZODIACPRKDC
Ontologies - Pathways
QuickGOP78527
Ontology : AmiGOtelomere maintenance  nuclear chromosome, telomeric region  somitogenesis  negative regulation of protein phosphorylation  activation of innate immune response  B cell lineage commitment  pro-B cell differentiation  T cell lineage commitment  negative regulation of immunoglobulin production  double-stranded DNA binding  RNA binding  protein kinase activity  protein kinase activity  protein serine/threonine kinase activity  protein serine/threonine kinase activity  protein serine/threonine kinase activity  DNA-dependent protein kinase activity  protein binding  ATP binding  nucleus  nucleus  nucleoplasm  nucleoplasm  transcription factor complex  nucleolus  cytosol  DNA-dependent protein kinase-DNA ligase 4 complex  double-strand break repair  double-strand break repair  double-strand break repair via nonhomologous end joining  cellular protein modification process  protein phosphorylation  protein phosphorylation  cellular response to DNA damage stimulus  cellular response to DNA damage stimulus  brain development  heart development  transcription factor binding  intrinsic apoptotic signaling pathway in response to DNA damage  response to gamma radiation  response to activity  membrane  telomere capping  protein ubiquitination  peptidyl-serine phosphorylation  enzyme binding  protein domain specific binding  protein destabilization  positive regulation of type I interferon production  cellular response to insulin stimulus  protein-containing complex  protein-DNA complex  T cell differentiation in thymus  immunoglobulin V(D)J recombination  T cell receptor V(D)J recombination  ectopic germ cell programmed cell death  regulation of circadian rhythm  positive regulation of apoptotic process  negative regulation of apoptotic process  innate immune response  positive regulation of transcription by RNA polymerase II  positive regulation of fibroblast proliferation  rhythmic process  spleen development  thymus development  positive regulation of developmental growth  regulation of smooth muscle cell proliferation  regulation of epithelial cell proliferation  nonhomologous end joining complex  signal transduction involved in mitotic G1 DNA damage checkpoint  double-strand break repair via alternative nonhomologous end joining  negative regulation of cellular senescence  positive regulation of double-strand break repair via nonhomologous end joining  negative regulation of response to gamma radiation  
Ontology : EGO-EBItelomere maintenance  nuclear chromosome, telomeric region  somitogenesis  negative regulation of protein phosphorylation  activation of innate immune response  B cell lineage commitment  pro-B cell differentiation  T cell lineage commitment  negative regulation of immunoglobulin production  double-stranded DNA binding  RNA binding  protein kinase activity  protein kinase activity  protein serine/threonine kinase activity  protein serine/threonine kinase activity  protein serine/threonine kinase activity  DNA-dependent protein kinase activity  protein binding  ATP binding  nucleus  nucleus  nucleoplasm  nucleoplasm  transcription factor complex  nucleolus  cytosol  DNA-dependent protein kinase-DNA ligase 4 complex  double-strand break repair  double-strand break repair  double-strand break repair via nonhomologous end joining  cellular protein modification process  protein phosphorylation  protein phosphorylation  cellular response to DNA damage stimulus  cellular response to DNA damage stimulus  brain development  heart development  transcription factor binding  intrinsic apoptotic signaling pathway in response to DNA damage  response to gamma radiation  response to activity  membrane  telomere capping  protein ubiquitination  peptidyl-serine phosphorylation  enzyme binding  protein domain specific binding  protein destabilization  positive regulation of type I interferon production  cellular response to insulin stimulus  protein-containing complex  protein-DNA complex  T cell differentiation in thymus  immunoglobulin V(D)J recombination  T cell receptor V(D)J recombination  ectopic germ cell programmed cell death  regulation of circadian rhythm  positive regulation of apoptotic process  negative regulation of apoptotic process  innate immune response  positive regulation of transcription by RNA polymerase II  positive regulation of fibroblast proliferation  rhythmic process  spleen development  thymus development  positive regulation of developmental growth  regulation of smooth muscle cell proliferation  regulation of epithelial cell proliferation  nonhomologous end joining complex  signal transduction involved in mitotic G1 DNA damage checkpoint  double-strand break repair via alternative nonhomologous end joining  negative regulation of cellular senescence  positive regulation of double-strand break repair via nonhomologous end joining  negative regulation of response to gamma radiation  
Pathways : KEGGNon-homologous end-joining    Cell cycle   
NDEx NetworkPRKDC
Atlas of Cancer Signalling NetworkPRKDC
Wikipedia pathwaysPRKDC
Orthology - Evolution
OrthoDB5591
GeneTree (enSembl)ENSG00000253729
Phylogenetic Trees/Animal Genes : TreeFamPRKDC
HOGENOMP78527
Homologs : HomoloGenePRKDC
Homology/Alignments : Family Browser (UCSC)PRKDC
Gene fusions - Rearrangements
Fusion : MitelmanKCMF1/PRKDC [2p11.2/8q11.21]  [t(2;8)(p11;q11)]  
Fusion : MitelmanPRKDC/C8orf22 [8q11.21/8q11.21]  [t(8;8)(q11;q11)]  
Fusion : MitelmanPRKDC/CEP290 [8q11.21/12q21.32]  [t(8;12)(q11;q21)]  
Fusion : MitelmanPRKDC/MYO5A [8q11.21/15q21.2]  [t(8;15)(q11;q21)]  
Fusion : MitelmanPRKDC/UBE2V2 [8q11.21/8q11.21]  [t(8;8)(q11;q11)]  
Fusion : MitelmanSLC39A14/PRKDC [8p21.3/8q11.21]  [t(8;8)(p21;q11)]  
Fusion PortalKCMF1 2p11.2 PRKDC 8q11.21 BRCA
Fusion PortalPRKDC 8q11.21 CEP290 12q21.32 BRCA
Fusion PortalPRKDC 8q11.21 MYO5A 15q21.2 LUAD
Fusion PortalPRKDC 8q11.21 UBE2V2 8q11.21 PRAD
Fusion PortalSLC39A14 8p21.3 PRKDC 8q11.21 BRCA
Fusion : QuiverPRKDC
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPRKDC [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PRKDC
dbVarPRKDC
ClinVarPRKDC
1000_GenomesPRKDC 
Exome Variant ServerPRKDC
ExAC (Exome Aggregation Consortium)ENSG00000253729
GNOMAD BrowserENSG00000253729
Varsome BrowserPRKDC
Genetic variants : HAPMAP5591
Genomic Variants (DGV)PRKDC [DGVbeta]
DECIPHERPRKDC [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPRKDC 
Mutations
ICGC Data PortalPRKDC 
TCGA Data PortalPRKDC 
Broad Tumor PortalPRKDC
OASIS PortalPRKDC [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPRKDC  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DPRKDC
Mutations and Diseases : HGMDPRKDC
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)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
BioMutasearch PRKDC
DgiDB (Drug Gene Interaction Database)PRKDC
DoCM (Curated mutations)PRKDC (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PRKDC (select a term)
intoGenPRKDC
Cancer3DPRKDC(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600899    615966   
Orphanet21580   
DisGeNETPRKDC
MedgenPRKDC
Genetic Testing Registry PRKDC
NextProtP78527 [Medical]
TSGene5591
GENETestsPRKDC
Target ValidationPRKDC
Huge Navigator PRKDC [HugePedia]
snp3D : Map Gene to Disease5591
BioCentury BCIQPRKDC
ClinGenPRKDC
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5591
Chemical/Pharm GKB GenePA33776
Clinical trialPRKDC
Miscellaneous
canSAR (ICR)PRKDC (select the gene name)
DataMed IndexPRKDC
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePRKDC
EVEXPRKDC
GoPubMedPRKDC
iHOPPRKDC
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

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indexed on : Wed Nov 13 18:02:37 CET 2019
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