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DKC1 dyskerin pseudouridine synthase 1 [ Homo sapiens (human) ]

Gene ID: 1736, updated on 14-Jul-2019

Summary

Official Symbol
DKC1provided by HGNC
Official Full Name
dyskerin pseudouridine synthase 1provided by HGNC
Primary source
HGNC:HGNC:2890
See related
Ensembl:ENSG00000130826 MIM:300126
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]
Expression
Ubiquitous expression in bone marrow (RPKM 13.6), lymph node (RPKM 11.6) and 25 other tissues See more
Orthologs

Genomic context

See DKC1 in Genome Data Viewer
Location:
Xq28
Exon count:
14
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 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 Sharpr-MPRA regulatory region 12525 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 palmitoylated protein 1 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 37

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

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

Copy number response

Description
Copy number response
Triplosensitivity

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

ClinGen Genome Curation Page
Haploinsufficency

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

ClinGen Genome Curation PagePubMed

HIV-1 interactions

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 Interaction Database

Pathways from BioSystems

  • Cell Cycle, organism-specific biosystem (from REACTOME)
    Cell Cycle, organism-specific biosystem
    Cell Cycle
  • Chromosome Maintenance, organism-specific biosystem (from REACTOME)
    Chromosome Maintenance, organism-specific biosystemChromosome maintenance is critical for stable chromosome function in mammalian and other eukaryotic cells. Aspects of telomere maintenance and nucleosome assembly are covered here.
  • Extension of Telomeres, organism-specific biosystem (from REACTOME)
    Extension of Telomeres, organism-specific biosystemTelomerase acts as reverse transcriptase in the elongation of telomeres (Smogorzewska and de Lange 2004).
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • H/ACA ribonucleoprotein complex, organism-specific biosystem (from KEGG)
    H/ACA ribonucleoprotein complex, organism-specific biosystemStructural complex; Genetic information processing; RNA processing
  • H/ACA ribonucleoprotein complex, conserved biosystem (from KEGG)
    H/ACA ribonucleoprotein complex, conserved biosystemStructural complex; Genetic information processing; RNA processing
  • Regulation of Telomerase, organism-specific biosystem (from Pathway Interaction Database)
    Regulation of Telomerase, organism-specific biosystem
    Regulation of Telomerase
  • Ribosome biogenesis in eukaryotes, organism-specific biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, organism-specific biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • Ribosome biogenesis in eukaryotes, conserved biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, conserved biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • Telomere Extension By Telomerase, organism-specific biosystem (from REACTOME)
    Telomere Extension By Telomerase, organism-specific biosystemHumans, like most eukaryotic organisms, add direct repeats to the telomere using a specialized DNA polymerase called telomerase. Telomerase is a ribonucleoprotein (RNP) complex minimally composed of...
  • Telomere Maintenance, organism-specific biosystem (from REACTOME)
    Telomere Maintenance, organism-specific biosystemTelomeres are protein-DNA complexes at the ends of linear chromosomes that are important for genome stability. Telomeric DNA in humans, as in many eukaryotic organisms, consists of tandem repeats (B...
  • rRNA modification in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    rRNA modification in the nucleus and cytosol, organism-specific biosystemHuman ribosomal RNAs (rRNAs) contain about 200 residues that are enzymatically modified after transcription in the nucleolus (Maden and Khan 1977, Maden 1988, Maden and Hughes 1997, reviewed in Herna...
  • rRNA processing, organism-specific biosystem (from REACTOME)
    rRNA processing, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
  • rRNA processing in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    rRNA processing in the nucleus and cytosol, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ97620

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding IPI
Inferred from Physical Interaction
more info
PubMed 
box H/ACA snoRNA binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
pseudouridine synthase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pseudouridine synthase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
telomerase RNA binding IC
Inferred by Curator
more info
PubMed 
telomerase RNA binding IPI
Inferred from Physical Interaction
more info
PubMed 
telomerase activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to telomerase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
RNA processing TAS
Traceable Author Statement
more info
PubMed 
box H/ACA snoRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enzyme-directed rRNA pseudouridine synthesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA pseudouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of establishment of protein localization to telomere IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein localization to Cajal body HMP PubMed 
positive regulation of telomerase RNA localization to Cajal body HMP PubMed 
positive regulation of telomerase RNA localization to Cajal body IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of telomerase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of telomere maintenance via telomerase IEA
Inferred from Electronic Annotation
more info
 
rRNA processing TAS
Traceable Author Statement
more info
PubMed 
rRNA pseudouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
rRNA pseudouridine synthesis TAS
Traceable Author Statement
more info
 
regulation of telomerase RNA localization to Cajal body IMP
Inferred from Mutant Phenotype
more info
PubMed 
scaRNA localization to Cajal body IMP
Inferred from Mutant Phenotype
more info
PubMed 
snRNA pseudouridine synthesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
telomerase RNA stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
telomere maintenance via telomerase IDA
Inferred from Direct Assay
more info
PubMed 
telomere maintenance via telomerase IMP
Inferred from Mutant Phenotype
more info
PubMed 
telomere maintenance via telomerase TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
box H/ACA scaRNP complex TAS
Traceable Author Statement
more info
PubMed 
box H/ACA snoRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
box H/ACA snoRNP complex IDA
Inferred from Direct Assay
more info
PubMed 
box H/ACA snoRNP complex TAS
Traceable Author Statement
more info
PubMed 
box H/ACA telomerase RNP complex IDA
Inferred from Direct Assay
more info
PubMed 
box H/ACA telomerase RNP complex TAS
Traceable Author Statement
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
fibrillar center IDA
Inferred from Direct Assay
more info
 
nucleolus TAS
Traceable Author Statement
more info
PubMed 
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 
telomerase holoenzyme complex TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
H/ACA ribonucleoprotein complex subunit DKC1
Names
CBF5 homolog
H/ACA ribonucleoprotein complex subunit 4
dyskeratosis congenita 1, dyskerin
nopp140-associated protein of 57 kDa
nucleolar protein NAP57
nucleolar protein family A member 4
snoRNP protein DKC1

NCBI Reference Sequences (RefSeq)

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 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001142463.3NP_001135935.1  H/ACA ribonucleoprotein complex subunit DKC1 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)
    AC109993
    UniProtKB/Swiss-Prot
    O60832
    Conserved Domains (4) summary
    cd02572
    Location:88270
    PseudoU_synth_hDyskerin; Pseudouridine synthase, human dyskerin like
    TIGR00425
    Location:56381
    CBF5; rRNA pseudouridine synthase, putative
    pfam01472
    Location:297370
    PUA; PUA domain
    pfam08068
    Location:49106
    DKCLD; DKCLD (NUC011) domain
  2. NM_001288747.1NP_001275676.1  H/ACA ribonucleoprotein complex subunit DKC1 isoform 3

    See identical proteins and their annotated locations for 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
    Consensus CDS
    CCDS76062.1
    UniProtKB/Swiss-Prot
    O60832
    Related
    ENSP00000478387.1, ENST00000620277.4
    Conserved Domains (1) summary
    cl27547
    Location:56381
    TruB_N; TruB family pseudouridylate synthase (N terminal domain)
  3. NM_001363.5NP_001354.1  H/ACA ribonucleoprotein complex subunit DKC1 isoform 1

    See identical proteins and their annotated locations for NP_001354.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC109993
    Consensus CDS
    CCDS14761.1
    UniProtKB/Swiss-Prot
    O60832
    Related
    ENSP00000358563.5, ENST00000369550.10
    Conserved Domains (1) summary
    cl27547
    Location:56381
    TruB_N; TruB family pseudouridylate synthase (N terminal domain)

RNA

  1. NR_110021.2 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)
    AC109993
  2. NR_110022.2 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)
    AC109993
  3. NR_110023.2 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)
    AC109993

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

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