VRK1 VRK serine/threonine kinase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: VRK1provided by HGNC
Official Full Name: VRK serine/threonine kinase 1provided by HGNC
Primary source: HGNC:HGNC:12718
See related: Ensembl:ENSG00000100749 MIM:602168; AllianceGenome:HGNC:12718
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: PCH1; PCH1A; HMNR10
Summary: This gene encodes a member of the vaccinia-related kinase (VRK) family of serine/threonine protein kinases. This gene is widely expressed in human tissues and has increased expression in actively dividing cells, such as those in testis, thymus, fetal liver, and carcinomas. Its protein localizes to the nucleus and has been shown to promote the stability and nuclear accumulation of a transcriptionally active p53 molecule and, in vitro, to phosphorylate Thr18 of p53 and reduce p53 ubiquitination. This gene, therefore, may regulate cell proliferation. This protein also phosphorylates histone, casein, and the transcription factors ATF2 (activating transcription factor 2) and c-JUN. [provided by RefSeq, Jul 2008]
Expression: Broad expression in bone marrow (RPKM 15.9), testis (RPKM 12.9) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q32.2

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (96797382..96881609)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (91029172..91113426)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (97263719..97347946)

Chromosome 14 - NC_000014.9 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
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?

ALS-associated VRK1 R321C mutation causes proteostatic imbalance and mitochondrial defects in iPSC-derived motor neurons.
Title: ALS-associated VRK1 R321C mutation causes proteostatic imbalance and mitochondrial defects in iPSC-derived motor neurons.
VRK1 Regulates Sensitivity to Oxidative Stress by Altering Histone Epigenetic Modifications and the Nuclear Phosphoproteome in Tumor Cells.
Title: VRK1 Regulates Sensitivity to Oxidative Stress by Altering Histone Epigenetic Modifications and the Nuclear Phosphoproteome in Tumor Cells.
VRK1 promotes DNA-induced type I interferon production.
Title: VRK1 promotes DNA-induced type I interferon production.
Loss of VRK1 alters the nuclear phosphoproteome in the DNA damage response to doxorubicin.
Title: Loss of VRK1 alters the nuclear phosphoproteome in the DNA damage response to doxorubicin.
Downregulation of VRK1 Inhibits Progression of Lung Squamous Cell Carcinoma through DNA Damage.
Title: Downregulation of VRK1 Inhibits Progression of Lung Squamous Cell Carcinoma through DNA Damage.
VRK1 variants at the cross road of Cajal body neuropathogenic mechanisms in distal neuropathies and motor neuron diseases.
Title: VRK1 variants at the cross road of Cajal body neuropathogenic mechanisms in distal neuropathies and motor neuron diseases.
Downregulating vaccinia-related kinase 1 by luteolin suppresses ovarian cancer cell proliferation by activating the p53 signaling pathway.
Title: Downregulating vaccinia-related kinase 1 by luteolin suppresses ovarian cancer cell proliferation by activating the p53 signaling pathway.
Circvrk1 downregulation attenuates brain microvascular endothelial cell damage induced by oxygen-glucose deprivation through modulating the miR-150-5p/MLLT1 axis.
Title: Circvrk1 downregulation attenuates brain microvascular endothelial cell damage induced by oxygen-glucose deprivation through modulating the miR-150-5p/MLLT1 axis.
VRK1 Is a Synthetic-Lethal Target in VRK2-Deficient Glioblastoma.
Title: VRK1 Is a Synthetic-Lethal Target in VRK2-Deficient Glioblastoma.
VRK1 as a synthetic lethal target in VRK2 promoter-methylated cancers of the nervous system.
Title: VRK1 as a synthetic lethal target in VRK2 promoter-methylated cancers of the nervous system.

Submit: New GeneRIF Correction See all GeneRIFs (70)

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
Neuronopathy, distal hereditary motor, autosomal recessive 10 MedGen: C5882703 OMIM: 620542 GeneReviews: Not available	not available
Pontocerebellar hypoplasia type 1A MedGen: C1843504 OMIM: 607596 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome wide association study of SNP-, gene-, and pathway-based approaches to identify genes influencing susceptibility to Staphylococcus aureus infections. EBI GWAS Catalog EBI GWAS CatalogPubMed
Heritability and genetic association analysis of cognition in the&#x000a0;Diabetes Heart Study. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH48802 (e-PCR)
- UniSTS:76045

RH80743 (e-PCR)
- UniSTS:85058

RH44891 (e-PCR)
- UniSTS:65888

NoName (e-PCR)
- UniSTS:488073

SHGC-33619 (e-PCR)
- UniSTS:79297

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3-phosphoinositide-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables AMP-activated protein kinase activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables Rho-dependent protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables eukaryotic translation initiation factor 2alpha kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS1 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS121 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AT120 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AX kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H2AXS139 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BS14 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BS36 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S10 kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3S28 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S57 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T11 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T3 kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3T45 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T6 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H4S1 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone binding	IPI Inferred from Physical Interaction more info	PubMed
enables kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables nucleosomal DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein kinase binding	IDA Inferred from Direct Assay more info	PubMed
enables protein serine kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein serine/threonine kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein serine/threonine kinase activity	TAS Traceable Author Statement more info
enables ribosomal protein S6 kinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in Cajal body organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA damage response	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA damage response	IDA Inferred from Direct Assay more info	PubMed
involved_in Golgi disassembly	IDA Inferred from Direct Assay more info	PubMed
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic nuclear membrane disassembly	TAS Traceable Author Statement more info
involved_in neuron projection development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein localization to chromatin	IDA Inferred from Direct Assay more info	PubMed
involved_in protein autophosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein phosphorylation	TAS Traceable Author Statement more info	PubMed
involved_in regulation of neuron migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Cajal body	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi stack	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: serine/threonine-protein kinase VRK1

Names: vaccinia related kinase 1; vaccinia virus B1R-related kinase 1

NP_001397980.1

EC 2.7.11.1

NP_001397982.1

EC 2.7.11.1

NP_003375.1

EC 2.7.11.1

XP_016877114.1

EC 2.7.11.1

XP_016877115.1

EC 2.7.11.1

XP_047287708.1

EC 2.7.11.1

XP_047287709.1

EC 2.7.11.1

XP_047287710.1

EC 2.7.11.1

XP_047287711.1

EC 2.7.11.1

XP_047287712.1

EC 2.7.11.1

XP_054232665.1

EC 2.7.11.1

XP_054232666.1

EC 2.7.11.1

XP_054232667.1

EC 2.7.11.1

XP_054232668.1

EC 2.7.11.1

XP_054232669.1

EC 2.7.11.1

XP_054232670.1

EC 2.7.11.1

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

NG_016293.1 RefSeqGene

Range

5036..89263

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001411051.1 → NP_001397980.1 serine/threonine-protein kinase VRK1 isoform 2

Status: REVIEWED

Source sequence(s)

AL133168

Consensus CDS

CCDS91928.1

UniProtKB/TrEMBL

H0YJF7

Related

ENSP00000451412.2, ENST00000553683.2
NM_001411053.1 → NP_001397982.1 serine/threonine-protein kinase VRK1 isoform 3

Status: REVIEWED

Source sequence(s)

AL133168

Consensus CDS

CCDS91929.1

UniProtKB/TrEMBL

A0A7P0T838

Related

ENSP00000504933.1, ENST00000681195.1
NM_003384.3 → NP_003375.1 serine/threonine-protein kinase VRK1 isoform 1

See identical proteins and their annotated locations for NP_003375.1

Status: REVIEWED

Source sequence(s)

AL133168, BU535261, CA436761

Consensus CDS

CCDS9947.1

UniProtKB/Swiss-Prot

Q3SYL2, Q99986

UniProtKB/TrEMBL

A0A7P0T9E5, A8K245

Related

ENSP00000216639.3, ENST00000216639.8

Conserved Domains (1) summary

cd14122
Location:26 → 326

STKc_VRK1; Catalytic domain of the Serine/Threonine protein kinase, Vaccinia Related Kinase 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

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

96797382..96881609

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047431755.1 → XP_047287711.1 serine/threonine-protein kinase VRK1 isoform X3
XM_017021626.3 → XP_016877115.1 serine/threonine-protein kinase VRK1 isoform X6

UniProtKB/TrEMBL

A0A7P0T814, A0A7P0TB08

Related

ENSP00000506517.1, ENST00000679736.1
XM_047431752.1 → XP_047287708.1 serine/threonine-protein kinase VRK1 isoform X1
XM_017021625.2 → XP_016877114.1 serine/threonine-protein kinase VRK1 isoform X4

UniProtKB/TrEMBL

A0A7P0T9E5, A8K245
XM_047431754.1 → XP_047287710.1 serine/threonine-protein kinase VRK1 isoform X2
XM_047431756.1 → XP_047287712.1 serine/threonine-protein kinase VRK1 isoform X5
XM_047431753.1 → XP_047287709.1 serine/threonine-protein kinase VRK1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060938.1 Alternate T2T-CHM13v2.0

Range

91029172..91113426

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054376692.1 → XP_054232667.1 serine/threonine-protein kinase VRK1 isoform X3
XM_054376695.1 → XP_054232670.1 serine/threonine-protein kinase VRK1 isoform X6

UniProtKB/TrEMBL

A0A7P0TB08
XM_054376690.1 → XP_054232665.1 serine/threonine-protein kinase VRK1 isoform X1
XM_054376693.1 → XP_054232668.1 serine/threonine-protein kinase VRK1 isoform X4
XM_054376691.1 → XP_054232666.1 serine/threonine-protein kinase VRK1 isoform X2
XM_054376694.1 → XP_054232669.1 serine/threonine-protein kinase VRK1 isoform X5