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

    Gene ID: 1736, updated on 24-Sep-2023

    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; AllianceGenome:HGNC:2890
    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; CHINE1; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See DKC1 in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_03 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154762864..154777689)
    RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152999274..153014101)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153991139..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 Sharpr-MPRA regulatory region 13577 Neighboring gene small nucleolar RNA, H/ACA box 36A Neighboring gene microRNA 664b Neighboring gene small nucleolar RNA, H/ACA box 56 Neighboring gene MAGUK p55 scaffold 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 Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2023-06-14)

    ClinGen Genome Curation Page
    Haploinsufficency

    Little evidence for dosage pathogenicity (Last evaluated 2023-06-14)

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ97620

    Gene Ontology Provided by GOA

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

    NEW Try the new Transcript table

    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
      Consensus CDS
      CCDS94705.1
      UniProtKB/Swiss-Prot
      O60832
      UniProtKB/TrEMBL
      A0A8Q3SIY6, A0A8Q3WLC8
      Related
      ENSP00000512730.1, ENST00000696575.1
      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_001288747.2NP_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)
      AC109993
      UniProtKB/Swiss-Prot
      O60832
      UniProtKB/TrEMBL
      A0A8Q3SIX2
      Related
      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
      F5BSB3, O43845, O60832, Q96G67, Q9Y505
      UniProtKB/TrEMBL
      A0A8Q3WLC8
      Related
      ENSP00000358563.5, ENST00000369550.10
      Conserved Domains (1) summary
      TIGR00425
      Location:56381
      CBF5; rRNA pseudouridine synthase, putative

    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
      Related
      ENST00000696584.1
    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
      Related
      ENST00000696585.1
    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
      Related
      ENST00000696582.1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      154762864..154777689
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      152999274..153014101
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)