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DKC1 (dyskeratosis congenita 1, dyskerin)

Identity

HGNC (Hugo) DKC1
LocusID (NCBI) 1736
Location Xq28
Location_base_pair Starts at 153991031 and ends at 154005964 bp from pter ( according to hg19-Feb_2009)  [Mapping]
Local_order distal, DKC1 is between DXS1684 and DXS1108.
 
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
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

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.
  

External links

Nomenclature
HGNC (Hugo)DKC1   2890
Cards
AtlasDKC1ID157
Entrez_Gene (NCBI)DKC1  1736  dyskeratosis congenita 1, dyskerin
GeneCards (Weizmann)DKC1
Ensembl (Hinxton)ENSG00000130826 [Gene_View]  chrX:153991031-154005964 [Contig_View]  DKC1 [Vega]
AceView (NCBI)DKC1
Genatlas (Paris)DKC1
WikiGenes1736
SOURCE (Princeton)NM_001142463 NM_001363
Genomic and cartography
GoldenPath (UCSC)DKC1  -  Xq28   chrX:153991031-154005964 +  Xq28   [Description]    (hg19-Feb_2009)
EnsemblDKC1 - Xq28 [CytoView]
Mapping of homologs : NCBIDKC1 [Mapview]
OMIM300126   300240   305000   
Gene and transcription
Genbank (Entrez)AF067008 AK225077 AK307672 AM392631 AM392823
RefSeq transcript (Entrez)NM_001142463 NM_001363
RefSeq genomic (Entrez)AC_000155 NC_000023 NC_018934 NG_009780 NT_167198 NW_001842420 NW_003871103 NW_004929448
Consensus coding sequences : CCDS (NCBI)DKC1
Cluster EST : UnigeneHs.4747 [ NCBI ]
CGAP (NCI)Hs.4747
Alternative Splicing : Fast-db (Paris)GSHG0031929
Alternative Splicing GalleryENSG00000130826
Gene ExpressionDKC1 [ NCBI-GEO ]     DKC1 [ SEEK ]   DKC1 [ MEM ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO60832 (Uniprot)
NextProtO60832  [Medical]
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 ]   
Domaine pattern : Prosite (Expaxy)PUA (PS50890)   
Domains : Interpro (EBI)Dyskerin-like    PsdUridine_synth    PsdUridine_synth_cat_dom    PUA    PUA-like_domain    tRNA_PsdUridine_synth_B_fam    Uncharacterised_CHP00451   
Related proteins : CluSTrO60832
Domain families : Pfam (Sanger)DKCLD (PF08068)    PUA (PF01472)    TruB_N (PF01509)   
Domain families : Pfam (NCBI)pfam08068    pfam01472    pfam01509   
Domain families : Smart (EMBL)PUA (SM00359)  
DMDM Disease mutations1736
Blocks (Seattle)O60832
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
InParanoidO60832
Interologous Interaction database O60832
IntegromeDBDKC1
STRING (EMBL)DKC1
Ontologies - Pathways
Ontology : AmiGOtelomere maintenance  pseudouridine synthesis  telomerase activity  RNA binding  protein binding  nucleus  nucleoplasm  telomerase holoenzyme complex  nucleolus  nucleolus  cytoplasm  rRNA processing  RNA processing  telomere maintenance via telomerase  cell proliferation  pseudouridine synthase activity  Cajal body  
Ontology : EGO-EBItelomere maintenance  pseudouridine synthesis  telomerase activity  RNA binding  protein binding  nucleus  nucleoplasm  telomerase holoenzyme complex  nucleolus  nucleolus  cytoplasm  rRNA processing  RNA processing  telomere maintenance via telomerase  cell proliferation  pseudouridine synthase activity  Cajal body  
Pathways : KEGGRibosome biogenesis in eukaryotes   
REACTOMEDKC1
Protein Interaction DatabaseDKC1
Wikipedia pathwaysDKC1
Gene fusion - rearrangments
Polymorphisms : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)DKC1
SNP (GeneSNP Utah)DKC1
SNP : HGBaseDKC1
Genetic variants : HAPMAPDKC1
1000_GenomesDKC1 
ICGC programENSG00000130826 
Somatic Mutations in Cancer : COSMICDKC1 
CONAN: Copy Number AnalysisDKC1 
OrphanetDyskeratosis congenita
Mutations and Diseases : HGMDDKC1
OMIM300126    300240    305000   
GENETestsDKC1
Disease Genetic AssociationDKC1
Huge Navigator DKC1 [HugePedia]  DKC1 [HugeCancerGEM]
Genomic VariantsDKC1  DKC1 [DGVbeta]
Exome VariantDKC1
dbVarDKC1
ClinVarDKC1
snp3D : Map Gene to Disease1736
General knowledge
Homologs : HomoloGeneDKC1
Homology/Alignments : Family Browser (UCSC)DKC1
Phylogenetic Trees/Animal Genes : TreeFamDKC1
Chemical/Protein Interactions : CTD1736
Chemical/Pharm GKB GenePA27344
Clinical trialDKC1
Cancer Resource (Charite)ENSG00000130826
Other databases
Probes
Litterature
PubMed102 Pubmed reference(s) in Entrez
CoreMineDKC1
iHOPDKC1

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, Bˆ§chner 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
 
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written11-2002Claude Viguié

Citation

This paper should be referenced as such :
Viguié C . DKC1 (dyskeratosis congenita 1, dyskerin). Atlas Genet Cytogenet Oncol Haematol. November 2002 .
URL : http://AtlasGeneticsOncology.org/Genes/DKC1ID157.html

The various updated versions of this paper are referenced and archived by INIST as such :
http://documents.irevues.inist.fr/bitstream/2042/37924/1/11-2002-DKC1ID157.pdf   [ Bibliographic record ]

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri Apr 18 17:39:02 CEST 2014

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