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

Gene ID: 1736, updated on 27-Nov-2024

Summary

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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
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Genomic context

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See DKC1 in Genome Data Viewer
Location:
Xq28
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (154762864..154777689)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152999274..153014101)
RS_2024_09 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 ATAC-STARR-seq lymphoblastoid silent region 21115 Neighboring gene Sharpr-MPRA regulatory region 12525 Neighboring gene Sharpr-MPRA regulatory region 13577 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21116 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21117 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30069 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 ATAC-STARR-seq lymphoblastoid silent region 21119 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 37

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Dyskeratosis congenita with a novel genetic variant in the DKC1 gene: a case report. Ratnasamy V, et al. BMC Med Genet, 2018 May 25. PMID 29801475, Free PMC Article
  2. Hoyeraal-Hreidarsson syndrome with a DKC1 mutation identified by whole-exome sequencing. Lim BC, et al. Gene, 2014 Aug 10. PMID 24914498
  3. X-linked dyskeratosis congenita in Malaysia. Hamidah A, et al. Pediatr Blood Cancer, 2008 Feb. PMID 17417794
  4. Dyskerin expression in human fetal, adult and neoplastic intrahepatic bile ducts: correlations with cholangiocarcinoma aggressiveness. Vasuri F, et al. Histopathology, 2015 Jan. PMID 25367684
  5. Late presentation of X-linked dyskeratosis congenita with a missense mutation in codon 350 of the dyskerin protein. Mori N, et al. Eur J Dermatol, 2015 Jan-Feb. PMID 25499969

See all (283) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identifying and validating the roles of the cuproptosis-related gene DKC1 in cancer with a focus on esophageal carcinoma.
    Title: Identifying and validating the roles of the cuproptosis-related gene DKC1 in cancer with a focus on esophageal carcinoma.
  2. DKC1 aggravates gastric cancer cell migration and invasion through up-regulating the expression of TNFAIP6.
    Title: DKC1 aggravates gastric cancer cell migration and invasion through up-regulating the expression of TNFAIP6.
  3. A pan-cancer analysis of Dyskeratosis congenita 1 (DKC1) as a prognostic biomarker.
    Title: A pan-cancer analysis of Dyskeratosis congenita 1 (DKC1) as a prognostic biomarker.
  4. AC125611.3 promotes the progression of colon cancer by recruiting DKC1 to stabilize CTNNB1.
    Title: AC125611.3 promotes the progression of colon cancer by recruiting DKC1 to stabilize CTNNB1.
  5. New Insights into Dyskerin-CypA Interaction: Implications for X-Linked Dyskeratosis Congenita and Beyond.
    Title: New Insights into Dyskerin-CypA Interaction: Implications for X-Linked Dyskeratosis Congenita and Beyond.
  6. Evidence from a meta-analysis for the prognostic and clinicopathological importance of DKC1 in malignancies.
    Title: Evidence from a meta-analysis for the prognostic and clinicopathological importance of DKC1 in malignancies.
  7. Domain specific mutations in dyskerin disrupt 3' end processing of scaRNA13.
    Title: Domain specific mutations in dyskerin disrupt 3' end processing of scaRNA13.
  8. Human dyskerin binds to cytoplasmic H/ACA-box-containing transcripts affecting nuclear hormone receptor dependence.
    Title: Human dyskerin binds to cytoplasmic H/ACA-box-containing transcripts affecting nuclear hormone receptor dependence.
  9. Pseudogene fms-related tyrosine kinase 1 pseudogene 1 (FLT1P1) cooperates with RNA binding protein dyskeratosis congenita 1 (DKC1) to restrain trophoblast cell proliferation and angiogenesis by targeting fms-related tyrosine kinase 1 (FLT1) in preeclampsia.
    Title: Pseudogene fms-related tyrosine kinase 1 pseudogene 1 (FLT1P1) cooperates with RNA binding protein dyskeratosis congenita 1 (DKC1) to restrain trophoblast cell proliferation and angiogenesis by targeting fms-related tyrosine kinase 1 (FLT1) in preeclampsia.
  10. Dual Inhibition of DKC1 and MEK1/2 Synergistically Restrains the Growth of Colorectal Cancer Cells.
    Title: Dual Inhibition of DKC1 and MEK1/2 Synergistically Restrains the Growth of Colorectal Cancer Cells.
Submit: New GeneRIF Correction See all GeneRIFs (80)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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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

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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
  
enables pseudouridine synthase activity IMP
Inferred from Mutant Phenotype
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 sno(s)RNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  
involved_in positive regulation of telomerase RNA localization to Cajal body IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of positive regulation of telomere maintenance via telomerase IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of positive regulation of telomere maintenance via telomerase IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within protein localization to Cajal body HMP PubMed 
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
  
involved_in regulation of telomerase RNA localization to Cajal body IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within 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
  
involved_in telomerase RNA stabilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in telomerase holoenzyme complex assembly IEA
Inferred from Electronic Annotation
more info
  
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
  
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

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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
NP_001135935.1
NP_001275676.1
NP_001354.1

NCBI Reference Sequences (RefSeq)

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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_001142463.3 → NP_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/TrEMBL
    A0A8Q3SIY6, A0A8Q3WLC8
    Related
    ENSP00000512730.1, ENST00000696575.1
    Conserved Domains (4) summary
    cd02572
    Location:88 → 270
    PseudoU_synth_hDyskerin; Pseudouridine synthase, human dyskerin like
    TIGR00425
    Location:56 → 381
    CBF5; rRNA pseudouridine synthase, putative
    pfam01472
    Location:297 → 370
    PUA; PUA domain
    pfam08068
    Location:49 → 106
    DKCLD; DKCLD (NUC011) domain

  2. NM_001288747.2 → NP_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/TrEMBL
    A0A8Q3SIX2
    Related
    ENST00000620277.4
    Conserved Domains (1) summary
    cl27547
    Location:56 → 381
    TruB_N; TruB family pseudouridylate synthase (N terminal domain)

  3. NM_001363.5 → NP_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:56 → 381
    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_2024_08

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)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60832.3 GenPept UniProtKB/Swiss-Prot:O60832

Gene LinkOut

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