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Aliases for VRK1 Gene

Aliases for VRK1 Gene

  • Vaccinia Related Kinase 1 2 3 5
  • EC 2.7.11.1 4 61
  • Serine/Threonine-Protein Kinase VRK1 3
  • Vaccinia Virus B1R-Related Kinase 1 3
  • Vaccinia-Related Kinase 1 4
  • PCH1A 3
  • PCH1 3

External Ids for VRK1 Gene

Previous GeneCards Identifiers for VRK1 Gene

  • GC14P094774
  • GC14P091080
  • GC14P095253
  • GC14P096333
  • GC14P097263
  • GC14P077447

Summaries for VRK1 Gene

Entrez Gene Summary for VRK1 Gene

  • 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]

GeneCards Summary for VRK1 Gene

VRK1 (Vaccinia Related Kinase 1) is a Protein Coding gene. Diseases associated with VRK1 include Pontocerebellar Hypoplasia Type 1A and Pontocerebellar Hypoplasia Type 1. Among its related pathways are Nuclear Envelope Reassembly and Mitotic Prophase. GO annotations related to this gene include transferase activity, transferring phosphorus-containing groups and protein serine/threonine kinase activity. An important paralog of this gene is VRK2.

UniProtKB/Swiss-Prot for VRK1 Gene

  • Serine/threonine kinase involved in Golgi disassembly during the cell cycle: following phosphorylation by PLK3 during mitosis, required to induce Golgi fragmentation. Acts by mediating phosphorylation of downstream target protein. Phosphorylates Thr-18 of p53/TP53 and may thereby prevent the interaction between p53/TP53 and MDM2. Phosphorylates casein and histone H3. Phosphorylates BANF1: disrupts its ability to bind DNA, reduces its binding to LEM domain-containing proteins and causes its relocalization from the nucleus to the cytoplasm. Phosphorylates ATF2 which activates its transcriptional activity.

Gene Wiki entry for VRK1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VRK1 Gene

Genomics for VRK1 Gene

Regulatory Elements for VRK1 Gene

Enhancers for VRK1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH14G096821 0.6 ENCODE 18.9 +24.3 24335 0.9 ZNF366 SMARCA4 ZNF207 PRDM10 YBX1 ZBTB17 VRK1 GC14P096860
GH14G096849 0.5 ENCODE 22.2 +52.4 52413 0.6 ZBED1 EED ETV6 MNT CREM VRK1 GC14P096860
GH14G096796 1.1 ENCODE 8.3 +0.5 462 2.1 ARNT CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143 FOS VRK1 GC14P096860
GH14G096961 0.8 Ensembl ENCODE 8.1 +166.0 166033 2.8 CTCF ZNF766 ETV1 SPI1 GABPA VRK1 GC14P096964 LINC00618
GH14G096824 0.5 ENCODE 8.7 +27.3 27309 0.8 CBFB EED ZBTB33 DPF2 PRDM1 VRK1 GC14P096860
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VRK1 on UCSC Golden Path with GeneCards custom track

Promoters for VRK1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000072775 353 1401 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143 FOS

Genomic Location for VRK1 Gene

Chromosome:
14
Start:
96,797,304 bp from pter
End:
96,931,722 bp from pter
Size:
134,419 bases
Orientation:
Plus strand

Genomic View for VRK1 Gene

Genes around VRK1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VRK1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VRK1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VRK1 Gene

Proteins for VRK1 Gene

  • Protein details for VRK1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q99986-VRK1_HUMAN
    Recommended name:
    Serine/threonine-protein kinase VRK1
    Protein Accession:
    Q99986
    Secondary Accessions:
    • Q3SYL2

    Protein attributes for VRK1 Gene

    Size:
    396 amino acids
    Molecular mass:
    45476 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for VRK1 Gene

neXtProt entry for VRK1 Gene

Selected DME Specific Peptides for VRK1 Gene

Q99986:
  • YLGVPKYWGSG
  • EYVHGDIKA
  • KVEPSDNGPLF
  • DLEILGY
  • LDILEYIH
  • LVDYGLAYRY
  • FTELKFYQ

Post-translational modifications for VRK1 Gene

  • Autophosphorylated at various serine and threonine residues. Autophosphorylation does not impair its ability to phosphorylate p53/TP53. Phosphorylation by PLK3 leads to induction of Golgi fragmentation during mitosis.
  • Ubiquitination at posLast=8585, posLast=112112, Lys188, Lys301, isoforms=307, posLast=314314, and Lys329
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for VRK1 (VRK1)
  • Abcam antibodies for VRK1

Domains & Families for VRK1 Gene

Gene Families for VRK1 Gene

Protein Domains for VRK1 Gene

Suggested Antigen Peptide Sequences for VRK1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q99986

UniProtKB/Swiss-Prot:

VRK1_HUMAN :
  • Belongs to the protein kinase superfamily. CK1 Ser/Thr protein kinase family. VRK subfamily.
Family:
  • Belongs to the protein kinase superfamily. CK1 Ser/Thr protein kinase family. VRK subfamily.
genes like me logo Genes that share domains with VRK1: view

Function for VRK1 Gene

Molecular function for VRK1 Gene

GENATLAS Biochemistry:
vaccinia-related kinase 1,widely expressed
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + a protein = ADP + a phosphoprotein.
UniProtKB/Swiss-Prot EnzymeRegulation:
Active in presence of Mn(2+), Mg(2+) and Zn(2+), but is not functional with Ca(2+) or Cu(2+). Has a higher affinity for Mn(2+) than for Mg(2+). RAN inhibits its autophosphorylation and its ability to phosphorylate histone H3.
UniProtKB/Swiss-Prot Function:
Serine/threonine kinase involved in Golgi disassembly during the cell cycle: following phosphorylation by PLK3 during mitosis, required to induce Golgi fragmentation. Acts by mediating phosphorylation of downstream target protein. Phosphorylates Thr-18 of p53/TP53 and may thereby prevent the interaction between p53/TP53 and MDM2. Phosphorylates casein and histone H3. Phosphorylates BANF1: disrupts its ability to bind DNA, reduces its binding to LEM domain-containing proteins and causes its relocalization from the nucleus to the cytoplasm. Phosphorylates ATF2 which activates its transcriptional activity.

Enzyme Numbers (IUBMB) for VRK1 Gene

Gene Ontology (GO) - Molecular Function for VRK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004672 protein kinase activity IDA,IEA 22194607
GO:0004674 protein serine/threonine kinase activity TAS --
GO:0005515 protein binding IPI 15105425
GO:0005524 ATP binding IEA --
GO:0016301 kinase activity IEA --
genes like me logo Genes that share ontologies with VRK1: view
genes like me logo Genes that share phenotypes with VRK1: view

Human Phenotype Ontology for VRK1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for VRK1

CRISPR Products

miRNA for VRK1 Gene

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for VRK1
  • Applied Biological Materials Clones for VRK1

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for VRK1 Gene

Localization for VRK1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VRK1 Gene

Cytoplasm. Nucleus. Cytoplasm, cytoskeleton, spindle. Note=Dispersed throughout the cell but not located on mitotic spindle or chromatids during mitosis.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VRK1 gene
Compartment Confidence
nucleus 5
cytosol 5
golgi apparatus 5
cytoskeleton 3
mitochondrion 2

Gene Ontology (GO) - Cellular Components for VRK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 22194607
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA --
GO:0005795 Golgi stack IDA 19103756
genes like me logo Genes that share ontologies with VRK1: view

Pathways & Interactions for VRK1 Gene

genes like me logo Genes that share pathways with VRK1: view

Pathways by source for VRK1 Gene

SIGNOR curated interactions for VRK1 Gene

Activates:
Inactivates:
Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for VRK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006468 protein phosphorylation IEA,IDA 22194607
GO:0007049 cell cycle IEA --
GO:0007067 mitotic nuclear division IEA --
GO:0007077 mitotic nuclear envelope disassembly TAS --
GO:0007084 mitotic nuclear envelope reassembly TAS --
genes like me logo Genes that share ontologies with VRK1: view

Drugs & Compounds for VRK1 Gene

(1) Drugs for VRK1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine triphosphate Approved Nutra 0

(1) Additional Compounds for VRK1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with VRK1: view

Transcripts for VRK1 Gene

Unigene Clusters for VRK1 Gene

Vaccinia related kinase 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for VRK1
  • Applied Biological Materials Clones for VRK1

Alternative Splicing Database (ASD) splice patterns (SP) for VRK1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14
SP1: - -
SP2:
SP3: -
SP4:

Relevant External Links for VRK1 Gene

GeneLoc Exon Structure for
VRK1
ECgene alternative splicing isoforms for
VRK1

Expression for VRK1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VRK1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for VRK1 Gene

This gene is overexpressed in Testis (12.8), Peripheral blood mononuclear cells (10.9), Blymphocyte (9.0), and CD8 Tcells (7.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VRK1 Gene



Protein tissue co-expression partners for VRK1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VRK1 Gene:

VRK1

SOURCE GeneReport for Unigene cluster for VRK1 Gene:

Hs.422662

mRNA Expression by UniProt/SwissProt for VRK1 Gene:

Q99986-VRK1_HUMAN
Tissue specificity: Widely expressed. Highly expressed in fetal liver, testis and thymus.

Evidence on tissue expression from TISSUES for VRK1 Gene

  • Nervous system(4.5)
  • Liver(4.2)
  • Lung(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VRK1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • tongue
Thorax:
  • chest wall
  • clavicle
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • abdominal wall
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • peripheral nerve
  • peripheral nervous system
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with VRK1: view

Primer Products

No data available for mRNA differential expression in normal tissues for VRK1 Gene

Orthologs for VRK1 Gene

This gene was present in the common ancestor of animals.

Orthologs for VRK1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VRK1 34 35
  • 99.49 (n)
cow
(Bos Taurus)
Mammalia VRK1 34 35
  • 90.4 (n)
dog
(Canis familiaris)
Mammalia VRK1 34 35
  • 90.07 (n)
rat
(Rattus norvegicus)
Mammalia Vrk1 34
  • 85.44 (n)
mouse
(Mus musculus)
Mammalia Vrk1 34 16 35
  • 83.76 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia VRK1 35
  • 82 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VRK1 35
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves VRK1 34 35
  • 73.76 (n)
lizard
(Anolis carolinensis)
Reptilia VRK1 35
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia vrk1 34
  • 68.37 (n)
MGC75762 34
African clawed frog
(Xenopus laevis)
Amphibia vrk1-prov 34
zebrafish
(Danio rerio)
Actinopterygii vrk1 34 35
  • 64.33 (n)
wufe16f06 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4919 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001933 34
  • 46.81 (n)
fruit fly
(Drosophila melanogaster)
Insecta BcDNA:LD09009 36
  • 41 (a)
ball 35
  • 25 (a)
ManyToMany
CG8878 35
  • 12 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea vrk-1 34 35
  • 46.02 (n)
F28B12.3 36
  • 33 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6830 35
  • 47 (a)
OneToMany
Species where no ortholog for VRK1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VRK1 Gene

ENSEMBL:
Gene Tree for VRK1 (if available)
TreeFam:
Gene Tree for VRK1 (if available)

Paralogs for VRK1 Gene

(3) SIMAP similar genes for VRK1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with VRK1: view

Variants for VRK1 Gene

Sequence variations from dbSNP and Humsavar for VRK1 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs137853063 Pathogenic 96,876,033(+) AGAAG(C/T)GAAAG nc-transcript-variant, reference, stop-gained
rs387906830 Pathogenic 96,852,853(+) TGGAT(C/T)GCTTT nc-transcript-variant, reference, missense
rs771364038 Pathogenic 96,855,353(+) ATGGC(A/G/T)TGGGT nc-transcript-variant, reference, missense
rs773138218 Pathogenic 96,846,144(+) CCAAC(A/G)AGCTG nc-transcript-variant, reference, missense
rs869312959 Pathogenic 96,860,736(+) CAAAG(A/G)TGAAT utr-variant-3-prime, splice-donor-variant

Structural Variations from Database of Genomic Variants (DGV) for VRK1 Gene

Variant ID Type Subtype PubMed ID
dgv1964n100 CNV gain 25217958
esv3303068 CNV tandem duplication 20981092
esv3581399 CNV loss 25503493
esv3635428 CNV loss 21293372
nsv1043916 CNV gain 25217958
nsv1051182 CNV loss 25217958
nsv510650 CNV deletion 20534489

Variation tolerance for VRK1 Gene

Residual Variation Intolerance Score: 29.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.83; 17.32% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for VRK1 Gene

Human Gene Mutation Database (HGMD)
VRK1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VRK1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VRK1 Gene

Disorders for VRK1 Gene

MalaCards: The human disease database

(14) MalaCards diseases for VRK1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
pontocerebellar hypoplasia type 1a
  • pontocerebellar hypoplasia 1a
pontocerebellar hypoplasia type 1
  • pontocerebellar hypoplasia with anterior horn cell disease
microcephaly-complex motor and sensory axonal neuropathy syndrome
vaccinia
pontocerebellar hypoplasia type 5
  • pontocerebellar hypoplasia, type 5
- elite association - COSMIC cancer census association via MalaCards
Search VRK1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

VRK1_HUMAN
  • Pontocerebellar hypoplasia 1A (PCH1A) [MIM:607596]: A disorder characterized by an abnormally small cerebellum and brainstem, central and peripheral motor dysfunction from birth, gliosis and spinal cord anterior horn cells degeneration resembling infantile spinal muscular atrophy. Additional features include muscle hypotonia, congenital contractures and respiratory insufficiency that is evident at birth. {ECO:0000269 PubMed:19646678}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VRK1

Genetic Association Database (GAD)
VRK1
Human Genome Epidemiology (HuGE) Navigator
VRK1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VRK1
genes like me logo Genes that share disorders with VRK1: view

No data available for Genatlas for VRK1 Gene

Publications for VRK1 Gene

  1. Spinal muscular atrophy with pontocerebellar hypoplasia is caused by a mutation in the VRK1 gene. (PMID: 19646678) Renbaum P. … Levy-Lahad E. (Am. J. Hum. Genet. 2009) 3 4 22 64
  2. Proteomics identification of nuclear Ran GTPase as an inhibitor of human VRK1 and VRK2 (vaccinia-related kinase) activities. (PMID: 18617507) Sanz-Garcia M. … Lazo P.A. (Mol. Cell. Proteomics 2008) 3 4 22 64
  3. Characterization of three paralogous members of the Mammalian vaccinia related kinase family. (PMID: 14645249) Nichols R.J. … Traktman P. (J. Biol. Chem. 2004) 3 4 22 64
  4. Human vaccinia-related kinase 1 (VRK1) activates the ATF2 transcriptional activity by novel phosphorylation on Thr-73 and Ser-62 and cooperates with JNK. (PMID: 15105425) Sevilla A. … Lazo P.A. (J. Biol. Chem. 2004) 3 4 22 64
  5. Kinetic properties of p53 phosphorylation by the human vaccinia- related kinase 1. (PMID: 11883897) Barcia R. … Lazo P.A. (Arch. Biochem. Biophys. 2002) 3 4 22 64

Products for VRK1 Gene

  • Addgene plasmids for VRK1

Sources for VRK1 Gene

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