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

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: mouse all
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Genomic context

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_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
Domain specific mutations in dyskerin disrupt 3' end processing of scaRNA13.
Title: Domain specific mutations in dyskerin disrupt 3' end processing of scaRNA13.
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.
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.
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

Associated conditions

Description	Tests
Cataracts, hearing impairment, nephrotic syndrome, and enterocolitis 1 MedGen: C5829571 OMIM: 301108 GeneReviews: Not available	not available
Dyskeratosis congenita, X-linked MedGen: C1148551 OMIM: 305000 GeneReviews: Dyskeratosis Congenita and Related Telomere Biology Disorders	not available
Hoyeraal-Hreidarsson syndrome MedGen: C1846142 GeneReviews: Not available	not available

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 variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

ECD08242 (e-PCR)
- UniSTS:289290

ECD18018 (e-PCR)
- UniSTS:299029

IB1223 (e-PCR)
- UniSTS:64040

ECD11405 (e-PCR)
- UniSTS:292441

stSG604276 (e-PCR)
- UniSTS:447593

ECD07325 (e-PCR)
- UniSTS:288380

ECD18896 (e-PCR)
- UniSTS:299906

ECD10168 (e-PCR)
- UniSTS:291208

REN90571 (e-PCR)
- UniSTS:415369

REN90572 (e-PCR)
- UniSTS:415370

REN90573 (e-PCR)
- UniSTS:415371

REN90574 (e-PCR)
- UniSTS:415372

REN90575 (e-PCR)
- UniSTS:415373

REN90576 (e-PCR)
- UniSTS:415374

REN90577 (e-PCR)
- UniSTS:415375

ECD15062 (e-PCR)
- UniSTS:296079

REN90578 (e-PCR)
- UniSTS:415376

ECD15063 (e-PCR)
- UniSTS:296080

REN90579 (e-PCR)
- UniSTS:415377

REN90580 (e-PCR)
- UniSTS:415378

REN90581 (e-PCR)
- UniSTS:415379

REN90582 (e-PCR)
- UniSTS:415380

REN90583 (e-PCR)
- UniSTS:415381

REN90584 (e-PCR)
- UniSTS:415382

REN90585 (e-PCR)
- UniSTS:415383

REN90586 (e-PCR)
- UniSTS:415384

REN90587 (e-PCR)
- UniSTS:415385

REN90588 (e-PCR)
- UniSTS:415386

ECD11985 (e-PCR)
- UniSTS:293018

REN90589 (e-PCR)
- UniSTS:415387

REN90590 (e-PCR)
- UniSTS:415388

REN90591 (e-PCR)
- UniSTS:415389

REN90592 (e-PCR)
- UniSTS:415390

REN90593 (e-PCR)
- UniSTS:415391

REN90594 (e-PCR)
- UniSTS:415392

REN90595 (e-PCR)
- UniSTS:415393

REN90596 (e-PCR)
- UniSTS:415394

REN90597 (e-PCR)
- UniSTS:415395

REN90598 (e-PCR)
- UniSTS:415396

REN90599 (e-PCR)
- UniSTS:415397

REN90600 (e-PCR)
- UniSTS:415398

REN90601 (e-PCR)
- UniSTS:415399

REN90602 (e-PCR)
- UniSTS:415400

REN90603 (e-PCR)
- UniSTS:415401

REN90604 (e-PCR)
- UniSTS:415402

REN90605 (e-PCR)
- UniSTS:415403

REN90606 (e-PCR)
- UniSTS:415404

REN90607 (e-PCR)
- UniSTS:415405

REN90608 (e-PCR)
- UniSTS:415406

REN90609 (e-PCR)
- UniSTS:415407

ECD09694 (e-PCR)
- UniSTS:290735

REN90610 (e-PCR)
- UniSTS:415408

REN90611 (e-PCR)
- UniSTS:415409

ECD09953 (e-PCR)
- UniSTS:290993

REN90612 (e-PCR)
- UniSTS:415410

REN90613 (e-PCR)
- UniSTS:415411

ECD00413 (e-PCR)
- UniSTS:281524

REN90614 (e-PCR)
- UniSTS:415412

REN90615 (e-PCR)
- UniSTS:415413

REN90616 (e-PCR)
- UniSTS:415414

REN90617 (e-PCR)
- UniSTS:415415

REN90618 (e-PCR)
- UniSTS:415416

REN90619 (e-PCR)
- UniSTS:415417

REN90620 (e-PCR)
- UniSTS:415418

REN90621 (e-PCR)
- UniSTS:415419

REN90622 (e-PCR)
- UniSTS:415420

REN90623 (e-PCR)
- UniSTS:415421

REN90624 (e-PCR)
- UniSTS:415422

REN90625 (e-PCR)
- UniSTS:415423

REN90626 (e-PCR)
- UniSTS:415424

REN90627 (e-PCR)
- UniSTS:415425

REN90628 (e-PCR)
- UniSTS:415426

REN90629 (e-PCR)
- UniSTS:415427

REN90630 (e-PCR)
- UniSTS:415428

REN90631 (e-PCR)
- UniSTS:415429

REN90632 (e-PCR)
- UniSTS:415430

REN90633 (e-PCR)
- UniSTS:415431

REN90634 (e-PCR)
- UniSTS:415432

REN90635 (e-PCR)
- UniSTS:415433

REN90636 (e-PCR)
- UniSTS:415434

REN90637 (e-PCR)
- UniSTS:415435

REN90638 (e-PCR)
- UniSTS:415436

REN90639 (e-PCR)
- UniSTS:415437

ECD13062 (e-PCR)
- UniSTS:294093

REN90640 (e-PCR)
- UniSTS:415438

ECD14101 (e-PCR)
- UniSTS:295126

A004F19 (e-PCR)
- UniSTS:4842

ECD06413 (e-PCR)
- UniSTS:287473

ECD06938 (e-PCR)
- UniSTS:287996

ECD11313 (e-PCR)
- UniSTS:292349

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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 more info	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 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

EC 5.4.99.-

NP_001275676.1

EC 5.4.99.-

NP_001354.1

EC 5.4.99.-

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

NG_009780.1 RefSeqGene

Range

4987..19934

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_55

mRNA and Protein(s)

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
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)
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

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
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
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