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DEK (DEK proto-oncogene)

Written1998-01Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

HGNC (Hugo) DEK
HGNC Alias symbD6S231E
HGNC Previous nameDEK oncogene (DNA binding)
 DEK oncogene
LocusID (NCBI) 7913
Atlas_Id 23
Location 6p22.3  [Link to chromosome band 6p22]
Location_base_pair Starts at 18223860 and ends at 18264530 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping DEK.png]
 
  DEK (6p23) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics.
 
  DEK (DEK proto-oncogene) Hybridization with DEK / NUP214 t(6;9) probe (Kreatech, Leica Biosystems Inc., US) showing DEK gene on 6p22.3 (green signals - Courtesy Adriana Zamecnikova.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
CABIN1 (22q11.23)::DEK (6p22.3)DEK (6p22.3)::CABIN1 (22q11.23)DEK (6p22.3)::CD164 (6q21)
DEK (6p22.3)::DEK (6p22.3)DEK (6p22.3)::EIF5B (2q11.2)DEK (6p22.3)::NUP214 (9q34.13)
EYS (6q12)::DEK (6p22.3)GRN (17q21.31)::DEK (6p22.3)LUC7L3 (17q21.33)::DEK (6p22.3)
NUP214 (9q34.13)::DEK (6p22.3)STAU2 (8q21.11)::DEK (6p22.3)

DNA/RNA

Description spans on a 40 kb genomic segment
Transcription 2.7 kb mRNA; coding sequence: 1.1 kb

Protein

Description 375 amino acids; 43 kDa; contains numerous acidic domains (Asp/Glu rich) and a nuclear localisation signal
Expression wide
Localisation potentially nuclear
Function site specific DNA binding protein involved in transcriptional regulation and signal transduction

Implicated in

Note
  
Entity /AML or MDS --> DEK-CAN
Disease M2, M4 AML or MDS
Prognosis remission difficult to obtain
Cytogenetics this chromosome anomaly may be over loocked
Hybrid/Mutated Gene 5' DEK - 3' CAN; chromosome 6 breakpoint clusters in a single intron
Abnormal Protein head to tail DEK/CAN fusion protein (the alternative SET/CAN is exceptional); almost the entire DEK protein fused to the C-terminal two-thirds of the CAN protein; nuclear localization
  

Bibliography

Interaction of cellular proteins with the leukemia specific fusion proteins DEK-CAN and SET-CAN and their normal counterpart, the nucleoporin CAN.
Fornerod M, Boer J, van Baal S, Morreau H, Grosveld G
Oncogene. 1996 ; 13 (8) : 1801-1808.
PMID 8895527
 
DEK, an autoantigen involved in a chromosomal translocation in acute myelogenous leukemia, binds to the HIV-2 enhancer.
Fu GK, Grosveld G, Markovitz DM
Proceedings of the National Academy of Sciences of the United States of America. 1997 ; 94 (5) : 1811-1815.
PMID 9050861
 
The translocation (6;9), associated with a specific subtype of acute myeloid leukemia, results in the fusion of two genes, dek and can, and the expression of a chimeric, leukemia-specific dek-can mRNA.
von Lindern M, Fornerod M, van Baal S, Jaegle M, de Wit T, Buijs A, Grosveld G
Molecular and cellular biology. 1992 ; 12 (4) : 1687-1697.
PMID 1549122
 

Citation

This paper should be referenced as such :
Jean-Loup Huret
DEK (DEK oncogene)
Atlas Genet Cytogenet Oncol Haematol. 1998;2(1):5-5.
Free journal version : [ pdf ]   [ DOI ]


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 4 ]
  NUP214::ABL1 fusion gene on amplified episomes
Classification of myelodysplastic syndromes 2015
t(6;9)(p22;q34) DEK::NUP214
t(6;9)(p22;q34) DEK::NUP214 in Childhood


External links

 

Nomenclature
HGNC (Hugo)DEK   2768
Cards
AtlasDEKID23
Entrez_Gene (NCBI)DEK    DEK proto-oncogene
AliasesD6S231E
GeneCards (Weizmann)DEK
Ensembl hg19 (Hinxton)ENSG00000124795 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000124795 [Gene_View]  ENSG00000124795 [Sequence]  chr6:18223860-18264530 [Contig_View]  DEK [Vega]
ICGC DataPortalENSG00000124795
TCGA cBioPortalDEK
AceView (NCBI)DEK
Genatlas (Paris)DEK
SOURCE (Princeton)DEK
Genetics Home Reference (NIH)DEK
Genomic and cartography
GoldenPath hg38 (UCSC)DEK  -     chr6:18223860-18264530 -  6p22.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)DEK  -     6p22.3   [Description]    (hg19-Feb_2009)
GoldenPathDEK - 6p22.3 [CytoView hg19]  DEK - 6p22.3 [CytoView hg38]
ImmunoBaseENSG00000124795
Genome Data Viewer NCBIDEK [Mapview hg19]  
OMIM125264   
Gene and transcription
Genbank (Entrez)AJ270688 AJ420539 AK294079 AK297749 AK298089
RefSeq transcript (Entrez)NM_001134709 NM_003472
Consensus coding sequences : CCDS (NCBI)DEK
Gene ExpressionDEK [ NCBI-GEO ]   DEK [ EBI - ARRAY_EXPRESS ]   DEK [ SEEK ]   DEK [ MEM ]
Gene Expression Viewer (FireBrowse)DEK [ Firebrowse - Broad ]
GenevisibleExpression of DEK in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)7913
GTEX Portal (Tissue expression)DEK
Human Protein AtlasENSG00000124795-DEK [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP35659   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP35659  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP35659
PhosPhoSitePlusP35659
Domains : Interpro (EBI)DEK_C    SAP_dom    SAP_dom_sf   
Domain families : Pfam (Sanger)DEK_C (PF08766)   
Domain families : Pfam (NCBI)pfam08766   
Domain families : Smart (EMBL)SAP (SM00513)  
Conserved Domain (NCBI)DEK
PDB (RSDB)1Q1V    2JX3   
PDB Europe1Q1V    2JX3   
PDB (PDBSum)1Q1V    2JX3   
PDB (IMB)1Q1V    2JX3   
Structural Biology KnowledgeBase1Q1V    2JX3   
SCOP (Structural Classification of Proteins)1Q1V    2JX3   
CATH (Classification of proteins structures)1Q1V    2JX3   
SuperfamilyP35659
AlphaFold pdb e-kbP35659   
Human Protein Atlas [tissue]ENSG00000124795-DEK [tissue]
HPRD00503
Protein Interaction databases
DIP (DOE-UCLA)P35659
IntAct (EBI)P35659
Complex Portal (EBI)P35659 CPX-1099 B-WICH chromatin remodelling complex
BioGRIDDEK
STRING (EMBL)DEK
ZODIACDEK
Ontologies - Pathways
QuickGOP35659
Ontology : AmiGODNA binding  RNA binding  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  chromatin organization  regulation of transcription by RNA polymerase II  transcription by RNA polymerase II  signal transduction  viral genome replication  granulocyte differentiation  histone binding  histone binding  contractile fiber  positive regulation of gene expression, epigenetic  regulation of double-strand break repair  regulation of double-strand break repair  regulation of double-strand break repair via nonhomologous end joining  
Ontology : EGO-EBIDNA binding  RNA binding  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  chromatin organization  regulation of transcription by RNA polymerase II  transcription by RNA polymerase II  signal transduction  viral genome replication  granulocyte differentiation  histone binding  histone binding  contractile fiber  positive regulation of gene expression, epigenetic  regulation of double-strand break repair  regulation of double-strand break repair  regulation of double-strand break repair via nonhomologous end joining  
REACTOMEP35659 [protein]
REACTOME PathwaysR-HSA-8864260 [pathway]   
NDEx NetworkDEK
Atlas of Cancer Signalling NetworkDEK
Wikipedia pathwaysDEK
Orthology - Evolution
OrthoDB7913
GeneTree (enSembl)ENSG00000124795
Phylogenetic Trees/Animal Genes : TreeFamDEK
Homologs : HomoloGeneDEK
Homology/Alignments : Family Browser (UCSC)DEK
Gene fusions - Rearrangements
Fusion : MitelmanDEK::NUP214 [6p22.3/9q34.13]  
Fusion : MitelmanEYS::DEK [6q12/6p22.3]  
Fusion : QuiverDEK
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerDEK [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)DEK
dbVarDEK
ClinVarDEK
MonarchDEK
1000_GenomesDEK 
Exome Variant ServerDEK
GNOMAD BrowserENSG00000124795
Varsome BrowserDEK
ACMGDEK variants
VarityP35659
Genomic Variants (DGV)DEK [DGVbeta]
DECIPHERDEK [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisDEK 
Mutations
ICGC Data PortalDEK 
TCGA Data PortalDEK 
Broad Tumor PortalDEK
OASIS PortalDEK [ Somatic mutations - Copy number]
Cancer Gene: CensusDEK 
Somatic Mutations in Cancer : COSMICDEK  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DDEK
Mutations and Diseases : HGMDDEK
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaDEK
DgiDB (Drug Gene Interaction Database)DEK
DoCM (Curated mutations)DEK
CIViC (Clinical Interpretations of Variants in Cancer)DEK
OncoKBDEK
NCG (London)DEK
Cancer3DDEK
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM125264   
Orphanet22869   
DisGeNETDEK
MedgenDEK
Genetic Testing Registry DEK
NextProtP35659 [Medical]
GENETestsDEK
Target ValidationDEK
Huge Navigator DEK [HugePedia]
ClinGenDEK
Clinical trials, drugs, therapy
MyCancerGenomeDEK
Protein Interactions : CTDDEK
Pharm GKB GenePA27251
PharosP35659
Clinical trialDEK
Miscellaneous
canSAR (ICR)DEK
HarmonizomeDEK
DataMed IndexDEK
Probes
Litterature
PubMed189 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXDEK
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri Oct 8 21:16:06 CEST 2021

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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.