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DKC1 dyskeratosis congenita 1, dyskerin [ Homo sapiens (human) ]

Gene ID: 1736, updated on 19-Jul-2014
Official Symbol
DKC1provided by HGNC
Official Full Name
dyskeratosis congenita 1, dyskerinprovided by HGNC
Primary source
HGNC:2890
See related
Ensembl:ENSG00000130826; HPRD:02129; MIM:300126; Vega:OTTHUMG00000024242
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DKC; CBF5; DKCX; NAP57; NOLA4; XAP101
Summary
This gene functions in two distinct complexes. It plays an active role in telomerase stabilization and maintenance, as well as recognition of snoRNAs containing H/ACA sequences which provides stability during biogenesis and assembly into H/ACA small nucleolar RNA ribonucleoproteins (snoRNPs). This gene is highly conserved and widely expressed, and may play additional roles in nucleo-cytoplasmic shuttling, DNA damage response, and cell adhesion. Mutations have been associated with X-linked dyskeratosis congenita. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
See DKC1 in Epigenomics, MapViewer
Location:
Xq28
Exon count:
14
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) X NC_000023.11 (154762742..154777689)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153991031..154005964)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene olfactory receptor, family 3, subfamily B, member 1 pseudogene Neighboring gene GRB2-associated binding protein 3 Neighboring gene small nucleolar RNA, H/ACA box 36A Neighboring gene microRNA 664b Neighboring gene small nucleolar RNA, H/ACA box 56 Neighboring gene membrane protein, palmitoylated 1, 55kDa Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 37

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Dyskeratosis congenita X-linked
MedGen: C1148551 OMIM: 305000 GeneReviews: Dyskeratosis Congenita
Compare labs
Hoyeraal Hreidarsson syndrome
MedGen: C1846142 OMIM: 300240 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-04-25)

ISCA Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated (2012-04-25)

ISCA Genome Curation PagePubMed

Replication interactions

Interaction Pubs
Knockdown of dyskeratosis congenita 1, dyskerin (DKC1) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Protein Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ97620

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding TAS
Traceable Author Statement
more info
PubMed 
poly(A) RNA binding IDA
Inferred from Direct Assay
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
pseudouridine synthase activity IEA
Inferred from Electronic Annotation
more info
 
telomerase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
RNA processing TAS
Traceable Author Statement
more info
PubMed 
cell proliferation TAS
Traceable Author Statement
more info
PubMed 
pseudouridine synthesis IEA
Inferred from Electronic Annotation
more info
 
rRNA processing IEA
Inferred from Electronic Annotation
more info
 
telomere maintenance TAS
Traceable Author Statement
more info
 
telomere maintenance via telomerase TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
Cajal body IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
NOT nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
telomerase holoenzyme complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
H/ACA ribonucleoprotein complex subunit 4
Names
H/ACA ribonucleoprotein complex subunit 4
CBF5 homolog
snoRNP protein DKC1
nucleolar protein NAP57
nucleolar protein family A member 4
nopp140-associated protein of 57 kDa

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009780.1 

    Range
    4987..19934
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_55

mRNA and Protein(s)

  1. NM_001142463.2NP_001135935.1  H/ACA ribonucleoprotein complex subunit 4 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK307672, BC009928, CD367400, HY050100
    UniProtKB/Swiss-Prot
    O60832
    Conserved Domains (4) summary
    cd02572
    Location:88270
    Blast Score: 924
    PseudoU_synth_hDyskerin; Pseudouridine synthase, human dyskerin like
    TIGR00425
    Location:56381
    Blast Score: 1413
    CBF5; rRNA pseudouridine synthase, putative
    pfam01472
    Location:297370
    Blast Score: 208
    PUA; PUA domain
    pfam08068
    Location:48106
    Blast Score: 297
    DKCLD; DKCLD (NUC011) domain
  2. NM_001288747.1NP_001275676.1  H/ACA ribonucleoprotein complex subunit 4 isoform 3

    See proteins identical to NP_001275676.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate 3' exon structure, which results in an early stop codon, compared to variant 1. The resulting protein (isoform 3) has a distinct C-terminus, compared to isoform 1 (PMID: 21820037).
    Source sequence(s)
    BC009928, CD367400, HY050100, JF279874
    UniProtKB/Swiss-Prot
    O60832
    Conserved Domains (4) summary
    cd02572
    Location:88270
    Blast Score: 921
    PseudoU_synth_hDyskerin; Pseudouridine synthase, human dyskerin like
    TIGR00425
    Location:56381
    Blast Score: 1415
    CBF5; rRNA pseudouridine synthase, putative
    pfam01472
    Location:297370
    Blast Score: 212
    PUA; PUA domain
    pfam08068
    Location:48106
    Blast Score: 299
    DKCLD; DKCLD (NUC011) domain
  3. NM_001363.4NP_001354.1  H/ACA ribonucleoprotein complex subunit 4 isoform 1

    See proteins identical to NP_001354.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK225077, BC009928, CD367400, HY050100
    Consensus CDS
    CCDS14761.1
    UniProtKB/Swiss-Prot
    O60832
    Related
    ENSP00000358563, OTTHUMP00000026046, ENST00000369550, OTTHUMT00000061180
    Conserved Domains (4) summary
    cd02572
    Location:88270
    Blast Score: 924
    PseudoU_synth_hDyskerin; Pseudouridine synthase, human dyskerin like
    TIGR00425
    Location:56381
    Blast Score: 1413
    CBF5; rRNA pseudouridine synthase, putative
    pfam01472
    Location:297370
    Blast Score: 208
    PUA; PUA domain
    pfam08068
    Location:48106
    Blast Score: 297
    DKCLD; DKCLD (NUC011) domain

RNA

  1. NR_110021.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, may render the transcript a candidate for nonsense-mediated mRNA decay (NMD). PMID: 24219293 indicates that this transcript may not be down-regulated by NMD; however, the potential to encode a truncated, but stable and functional protein has not been demonstrated.
    Source sequence(s)
    BC009928, CD367400, HY050100, KC954523
  2. NR_110022.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, may render the transcript a candidate for nonsense-mediated mRNA decay (NMD). PMID: 24219293 indicates that this transcript may not be down-regulated by NMD; however, the potential to encode a truncated, but stable and functional protein has not been demonstrated.
    Source sequence(s)
    BC009928, CD367400, HY050100, KC954524
  3. NR_110023.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, may render the transcript a candidate for nonsense-mediated mRNA decay (NMD). PMID: 24219293 indicates that this transcript may not be down-regulated by NMD; however, the potential to encode a truncated, but stable and functional protein has not been demonstrated.
    Source sequence(s)
    BC009928, CD367400, HY050100, KC954525

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000023.11 

    Range
    154762742..154777689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000155.1 

    Range
    142534579..142549324
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018934.2 

    Range
    153902709..153917646
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)