mutated Ligand Binding Site gene DataBase





About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for VRK1
Gene summary
Basic gene Info.Gene symbolVRK1
Gene namevaccinia related kinase 1
CytomapUCSC genome browser: 14q32
Type of geneprotein-coding
Descriptionserine/threonine-protein kinase VRK1vaccinia virus B1R-related kinase 1vaccinia-related kinase 1
Modification date20141207
dbXrefs MIM : 602168
Ensembl : ENSG00000100749
HPRD : 03701
Vega : OTTHUMG00000171459
ProteinUniProt: Q99986
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_VRK1
BioGPS: 7443
PathwayNCI Pathway Interaction Database: VRK1
Pathway Commons: VRK1
ContextiHOP: VRK1
ligand binding site mutation search in PubMed: VRK1
UCL Cancer Institute: VRK1
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0006468protein phosphorylation22194607
GO:0043987histone H3-S10 phosphorylation22194607
GO:0046777protein autophosphorylation21543316
GO:0072355histone H3-T3 phosphorylation22194607
GO:0090166Golgi disassembly19103756

Ligand binding site mutations for VRK1
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
: non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.

Protein structure related information for VRK1
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for VRK1 from PDB

Differential gene expression and gene-gene network for VRK1
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of VRK1 and the right PPI network was created from samples without mutations in the LBS of VRK1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for VRK1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1843504Pontocerebellar Hypoplasia Type 12Biomarker, GeneticVariation
umls:C3714756Intellectual Disability1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Pharmacological information for VRK1
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of VRK1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of VRK1
Multiple alignments for Q99986 in multiple species
LBSAA sequence# speciesSpecies
D132RFMIMDRFGSD2Homo sapiens, Mus musculus
D132RYMIIPKYATS1Caenorhabditis elegans
D132RFMVMDRFGTD1Danio rerio
D132RFMIIDRFGSD1Bos taurus
F134MIMDRFGSDLQ2Homo sapiens, Mus musculus
F134MIIPKYATSLE1Caenorhabditis elegans
F134MVMDRFGTDLQ1Danio rerio
F134MIIDRFGSDLQ1Bos taurus
F48IGQGGFGCIYL3Homo sapiens, Mus musculus, Bos taurus
F48FATGGFGRIHT1Caenorhabditis elegans
F48VGQGGFGLLYL1Danio rerio
I43KVGLPIGQGGF1Homo sapiens
I43IVGKQFATGGF1Caenorhabditis elegans
I43KLGSAVGQGGF1Danio rerio
I43KLGLPIGQGGF1Mus musculus
I51GGFGCIYLADM2Homo sapiens, Bos taurus
I51GGFGRIHTCTE1Caenorhabditis elegans
I51GGFGLLYLANE1Danio rerio
I51GGFGCIYLADT1Mus musculus
K71APCVVKVEPSD3Homo sapiens, Mus musculus, Bos taurus
K71QQMVMKIEPST1Caenorhabditis elegans
K71APYVIKVEPSD1Danio rerio
L184KASNLLLNYKN1Homo sapiens
L184KAANILLEKQG1Caenorhabditis elegans
L184KASNLLLSYTN1Danio rerio
L184KASNLLLSHKN1Mus musculus
L184KASNLLLSYKN1Bos taurus
M131YRFMIMDRFGS2Homo sapiens, Mus musculus
M131MRYMIIPKYAT1Caenorhabditis elegans
M131YRFMVMDRFGT1Danio rerio
M131YRFMIIDRFGS1Bos taurus
R133FMIMDRFGSDL2Homo sapiens, Mus musculus
R133YMIIPKYATSL1Caenorhabditis elegans
R133FMVMDRFGTDL1Danio rerio
R133FMIIDRFGSDL1Bos taurus
V196DQVYLVDYGLA3Homo sapiens, Mus musculus, Bos taurus
V196STAVLVDFGLA1Caenorhabditis elegans
V196NQVFLVDYGLA1Danio rerio
V69SDAPCVVKVEP2Homo sapiens, Mus musculus
V69KSQQMVMKIEP1Caenorhabditis elegans
V69ADAPYVIKVEP1Danio rerio
Y87TELKFYQRAAK3Homo sapiens, Mus musculus, Bos taurus
Y87TEVVVFNRILK1Caenorhabditis elegans
Y87SELKFYMRAAK1Danio rerio

Copyright © 2016-Present - The University of Texas Health Science Center at Houston
Site Policies | State of Texas