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DKC1 (dyskeratosis congenita 1, dyskerin)

Written2002-11Claude Viguié
Service de Dermatologie, Hôpital Tarnier-Cochin, 89 rue d'Assas, 75006 Paris, France

(Note : for Links provided by Atlas : click)

Identity

HGNC (Hugo) DKC1
LocusID (NCBI) 1736
Atlas_Id 157
Location Xq28
Location_base_pair Starts at 153991017 and ends at 154005964 bp from pter ( according to hg19-Feb_2009)  [Mapping DKC1.png]
Local_order distal, DKC1 is between DXS1684 and DXS1108.
 
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
Fusion genes
(updated 2016)
DKC1 (Xq28) / GCH1 (14q22.2)DKC1 (Xq28) / NKIRAS1 (3p24.2)
Note X-linked dyskeratosis congenita (genes for dominant and recessive autosomal forms have not been identified).

DNA/RNA

Description Gene composed of 15 exons (exons 1 and 15 non coding) / 15kb length cDNA 2465 bp (open reading frame between nt 93 and 1637)

Protein

Description Dyskerin, 514 amino acids, 57 kDa.
Expression widespread tissue expression.
Function Multifunctional nucleolar protein which associates with H+ACA (hairpin-linge hairpin-tail) class of small nucleolar RNA as its catalytic sub-unit; implicated in centromere function; associated also with the telomerase RNA component; function in ribosome biosynthesis
Homology highly conserved in eukaryotes: Nap57 (nucleolar associated protein) in the rat, Nop60B in drosophila, Cbf5p (centromere/microtubule binding protein) in yeast. Regional homologies with bacterial Trub proteins and Saccharomyces cerevisiae PUS4 protein.

Implicated in

Note
Disease Dyskeratosis congenita, X-linked recessive form
Hybrid/Mutated Gene missense mutation by single-nucleotide substitution at position 1058 in exon 11 (A353V) detected in several different families. Sporadic other missense mutations were detected in exon 3, 4, 10, 12 and in intron 2. Rare deletions and no null mutations are observed.
Abnormal Protein non functional protein. It is not presently known how the different mutations affect the protein activity and are responsible of the various phenotypes
Oncogenesis myelodysplasia and leukemia following bone marrow failure and pancytopenia. Spinocellular carcinoma, other carcinomas of various localization.
  

Bibliography

Dyskeratosis congenita caused by a 3' deletion: germline and somatic mosaicism in a female carrier.
Vulliamy TJ, Knight SW, Heiss NS, Smith OP, Poustka A, Dokal I, Mason PJ
Blood. 1999 ; 94 (4) : 1254-1260.
PMID 10438713
 
X-linked dyskeratosis congenita is predominantly caused by missense mutations in the DKC1 gene.
Knight SW, Heiss NS, Vulliamy TJ, Greschner S, Stavrides G, Pai GS, Lestringant G, Varma N, Mason PJ, Dokal I, Poustka A
American journal of human genetics. 1999 ; 65 (1) : 50-58.
PMID 10364516
 
Dyskeratosis congenita in all its forms.
Dokal I
British journal of haematology. 2000 ; 110 (4) : 768-779.
PMID 11054058
 
Gene structure and expression of the mouse dyskeratosis congenita gene, dkc1.
Heiss NS, Bächner D, Salowsky R, Kolb A, Kioschis P, Poustka A
Genomics. 2000 ; 67 (2) : 153-163.
PMID 10903840
 
The RNA component of telomerase is mutated in autosomal dominant dyskeratosis congenita.
Vulliamy T, Marrone A, Goldman F, Dearlove A, Bessler M, Mason PJ, Dokal I
Nature. 2001 ; 413 (6854) : 432-435.
PMID 11574891
 

Citation

This paper should be referenced as such :
Viguié, C
DKC1 (dyskeratosis congenita 1, dyskerin)
Atlas Genet Cytogenet Oncol Haematol. 2003;7(1):14-15.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/DKC1ID157.html


Other Cancer prone implicated (Data extracted from papers in the Atlas) [ 1 ]
  Dyskeratosis congenita (DKC)

External links

Nomenclature
HGNC (Hugo)DKC1   2890
Cards
AtlasDKC1ID157
Entrez_Gene (NCBI)DKC1  1736  dyskerin pseudouridine synthase 1
AliasesCBF5; DKC; DKCX; NAP57; 
NOLA4; XAP101
GeneCards (Weizmann)DKC1
Ensembl hg19 (Hinxton)ENSG00000130826 [Gene_View]  chrX:153991017-154005964 [Contig_View]  DKC1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000130826 [Gene_View]  chrX:153991017-154005964 [Contig_View]  DKC1 [Vega]
ICGC DataPortalENSG00000130826
TCGA cBioPortalDKC1
AceView (NCBI)DKC1
Genatlas (Paris)DKC1
WikiGenes1736
SOURCE (Princeton)DKC1
Genomic and cartography
GoldenPath hg19 (UCSC)DKC1  -     chrX:153991017-154005964 +  Xq28   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)DKC1  -     Xq28   [Description]    (hg38-Dec_2013)
EnsemblDKC1 - Xq28 [CytoView hg19]  DKC1 - Xq28 [CytoView hg38]
Mapping of homologs : NCBIDKC1 [Mapview hg19]  DKC1 [Mapview hg38]
OMIM300126   305000   
Gene and transcription
Genbank (Entrez)AF067008 AK225077 AK307672 AM392631 AM392823
RefSeq transcript (Entrez)NM_001142463 NM_001288747 NM_001363
RefSeq genomic (Entrez)NC_000023 NC_018934 NG_009780 NT_011681 NW_004929448
Consensus coding sequences : CCDS (NCBI)DKC1
Cluster EST : UnigeneHs.4747 [ NCBI ]
CGAP (NCI)Hs.4747
Alternative Splicing GalleryENSG00000130826
Gene ExpressionDKC1 [ NCBI-GEO ]   DKC1 [ EBI - ARRAY_EXPRESS ]   DKC1 [ SEEK ]   DKC1 [ MEM ]
Gene Expression Viewer (FireBrowse)DKC1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1736
GTEX Portal (Tissue expression)DKC1
Protein : pattern, domain, 3D structure
UniProt/SwissProtO60832 (Uniprot)
NextProtO60832  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO60832
Splice isoforms : SwissVarO60832 (Swissvar)
Catalytic activity : Enzyme5.4.99.- [ Enzyme-Expasy ]   5.4.99.-5.4.99.- [ IntEnz-EBI ]   5.4.99.- [ BRENDA ]   5.4.99.- [ KEGG ]   
PhosPhoSitePlusO60832
Domaine pattern : Prosite (Expaxy)PUA (PS50890)   
Domains : Interpro (EBI)Dyskerin-like    PsdUridine_synth_cat_dom    PsdUridine_synth_N    PUA    PUA-like_domain    tRNA_PsdUridine_synth_B_fam    TruB_C    Uncharacterised_CHP00451   
Domain families : Pfam (Sanger)DKCLD (PF08068)    PUA (PF01472)    TruB_C_2 (PF16198)    TruB_N (PF01509)   
Domain families : Pfam (NCBI)pfam08068    pfam01472    pfam16198    pfam01509   
Domain families : Smart (EMBL)PUA (SM00359)  
DMDM Disease mutations1736
Blocks (Seattle)DKC1
SuperfamilyO60832
Human Protein AtlasENSG00000130826
Peptide AtlasO60832
HPRD02129
IPIIPI00221394   IPI00915274   IPI00852712   IPI00852780   IPI00874145   IPI00893397   IPI00893630   
Protein Interaction databases
DIP (DOE-UCLA)O60832
IntAct (EBI)O60832
FunCoupENSG00000130826
BioGRIDDKC1
STRING (EMBL)DKC1
ZODIACDKC1
Ontologies - Pathways
QuickGOO60832
Ontology : AmiGObox H/ACA snoRNA 3'-end processing  telomerase activity  telomerase activity  RNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  telomerase holoenzyme complex  telomerase holoenzyme complex  nucleolus  cytoplasm  rRNA processing  RNA processing  telomere maintenance via telomerase  telomere maintenance via telomerase  cell proliferation  pseudouridine synthase activity  rRNA pseudouridine synthesis  rRNA pseudouridine synthesis  snRNA pseudouridine synthesis  box H/ACA snoRNP complex  box H/ACA snoRNP complex  positive regulation of telomere maintenance via telomerase  box H/ACA snoRNA binding  poly(A) RNA binding  positive regulation of telomerase activity  telomerase RNA binding  box H/ACA scaRNP complex  box H/ACA telomerase RNP complex  box H/ACA telomerase RNP complex  telomerase RNA stabilization  positive regulation of establishment of protein localization to telomere  positive regulation of telomerase RNA localization to Cajal body  mRNA pseudouridine synthesis  
Ontology : EGO-EBIbox H/ACA snoRNA 3'-end processing  telomerase activity  telomerase activity  RNA binding  protein binding  nucleus  nucleoplasm  nucleoplasm  telomerase holoenzyme complex  telomerase holoenzyme complex  nucleolus  cytoplasm  rRNA processing  RNA processing  telomere maintenance via telomerase  telomere maintenance via telomerase  cell proliferation  pseudouridine synthase activity  rRNA pseudouridine synthesis  rRNA pseudouridine synthesis  snRNA pseudouridine synthesis  box H/ACA snoRNP complex  box H/ACA snoRNP complex  positive regulation of telomere maintenance via telomerase  box H/ACA snoRNA binding  poly(A) RNA binding  positive regulation of telomerase activity  telomerase RNA binding  box H/ACA scaRNP complex  box H/ACA telomerase RNP complex  box H/ACA telomerase RNP complex  telomerase RNA stabilization  positive regulation of establishment of protein localization to telomere  positive regulation of telomerase RNA localization to Cajal body  mRNA pseudouridine synthesis  
Pathways : KEGGRibosome biogenesis in eukaryotes   
REACTOMEO60832 [protein]
REACTOME PathwaysR-HSA-171319 Telomere Extension By Telomerase [pathway]
NDEx Network
Atlas of Cancer Signalling NetworkDKC1
Wikipedia pathwaysDKC1
Orthology - Evolution
OrthoDB1736
GeneTree (enSembl)ENSG00000130826
Phylogenetic Trees/Animal Genes : TreeFamDKC1
Homologs : HomoloGeneDKC1
Homology/Alignments : Family Browser (UCSC)DKC1
Gene fusions - Rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerDKC1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)DKC1
dbVarDKC1
ClinVarDKC1
1000_GenomesDKC1 
Exome Variant ServerDKC1
ExAC (Exome Aggregation Consortium)DKC1 (select the gene name)
Genetic variants : HAPMAP1736
Genomic Variants (DGV)DKC1 [DGVbeta]
Mutations
ICGC Data PortalDKC1 
TCGA Data PortalDKC1 
Broad Tumor PortalDKC1
OASIS PortalDKC1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICDKC1 
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)Mendelian genes
LOVD (Leiden Open Variation Database)X-chromosome gene database
LOVD (Leiden Open Variation Database)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
BioMutasearch DKC1
DgiDB (Drug Gene Interaction Database)DKC1
DoCM (Curated mutations)DKC1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)DKC1 (select a term)
intoGenDKC1
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)X:153991017-154005964  ENSG00000130826
CONAN: Copy Number AnalysisDKC1 
OrphanetDyskeratosis congenita
Mutations and Diseases : HGMDDKC1
OMIM300126    305000   
MedgenDKC1
Genetic Testing Registry DKC1
NextProtO60832 [Medical]
TSGene1736
GENETestsDKC1
Huge Navigator DKC1 [HugePedia]
snp3D : Map Gene to Disease1736
BioCentury BCIQDKC1
ClinGenDKC1 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1736
Chemical/Pharm GKB GenePA27344
Clinical trialDKC1
Miscellaneous
canSAR (ICR)DKC1 (select the gene name)
Probes
Litterature
PubMed128 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineDKC1
EVEXDKC1
GoPubMedDKC1
iHOPDKC1
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 : Sat May 28 11:43:29 CEST 2016

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