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mutLBSgeneDB |
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| Gene summary for VRK1 |
 Gene summary |
| Basic gene Info. | Gene symbol | VRK1 |
| Gene name | vaccinia related kinase 1 | |
| Synonyms | PCH1|PCH1A | |
| Cytomap | UCSC genome browser: 14q32 | |
| Type of gene | protein-coding | |
| RefGenes | NM_003384.2, | |
| Description | serine/threonine-protein kinase VRK1vaccinia virus B1R-related kinase 1vaccinia-related kinase 1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 602168 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000100749 | ||
| HPRD : 03701 | ||
| Vega : OTTHUMG00000171459 | ||
| Protein | UniProt: Q99986 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_VRK1 | |
| BioGPS: 7443 | ||
| Pathway | NCI Pathway Interaction Database: VRK1 | |
| KEGG: VRK1 | ||
| REACTOME: VRK1 | ||
| Pathway Commons: VRK1 | ||
| Context | iHOP: VRK1 | |
| ligand binding site mutation search in PubMed: VRK1 | ||
| UCL Cancer Institute: VRK1 | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0006468 | protein phosphorylation | 22194607 | GO:0043987 | histone H3-S10 phosphorylation | 22194607 | GO:0046777 | protein autophosphorylation | 21543316 | GO:0072355 | histone H3-T3 phosphorylation | 22194607 | GO:0090166 | Golgi disassembly | 19103756 |
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| 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. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | Y87 | Q88L | LUSC | 1 | R133 | R133H | UCEC | 1 |
| 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. |
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| 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 |
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| 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. |
| LBS | AAchange of nsSNV | Relative stability change | Y87 | Q88L | 0.14301156 | R133 | R133H | -1.5629363 |
| (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 |
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| 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) |
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| Phenotype information for VRK1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C1843504 | Pontocerebellar Hypoplasia Type 1 | 2 | Biomarker, GeneticVariation |
| umls:C3714756 | Intellectual Disability | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| 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. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of VRK1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | REB | [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]PYRIMIDIN-2-YL}AMINO)PHENYL]ACETONITRILE | 3op5 | C | R133 | REB | [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]PYRIMIDIN-2-YL}AMINO)PHENYL]ACETONITRILE | 3op5 | D | R133 | REB | [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]PYRIMIDIN-2-YL}AMINO)PHENYL]ACETONITRILE | 3op5 | A | Y87 R133 | REB | [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]PYRIMIDIN-2-YL}AMINO)PHENYL]ACETONITRILE | 3op5 | B | Y87 R133 |
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| Conservation information for LBS of VRK1 |
| Multiple alignments for Q99986 in multiple species |
| LBS | AA sequence | # species | Species | D132 | RFMIMDRFGSD | 2 | Homo sapiens, Mus musculus | D132 | RYMIIPKYATS | 1 | Caenorhabditis elegans | D132 | RFMVMDRFGTD | 1 | Danio rerio | D132 | RFMIIDRFGSD | 1 | Bos taurus | F134 | MIMDRFGSDLQ | 2 | Homo sapiens, Mus musculus | F134 | MIIPKYATSLE | 1 | Caenorhabditis elegans | F134 | MVMDRFGTDLQ | 1 | Danio rerio | F134 | MIIDRFGSDLQ | 1 | Bos taurus | F48 | IGQGGFGCIYL | 3 | Homo sapiens, Mus musculus, Bos taurus | F48 | FATGGFGRIHT | 1 | Caenorhabditis elegans | F48 | VGQGGFGLLYL | 1 | Danio rerio | I43 | KVGLPIGQGGF | 1 | Homo sapiens | I43 | IVGKQFATGGF | 1 | Caenorhabditis elegans | I43 | KLGSAVGQGGF | 1 | Danio rerio | I43 | KLGLPIGQGGF | 1 | Mus musculus | I43 | KLGSPIGQGGF | 1 | Bos taurus | I51 | GGFGCIYLADM | 2 | Homo sapiens, Bos taurus | I51 | GGFGRIHTCTE | 1 | Caenorhabditis elegans | I51 | GGFGLLYLANE | 1 | Danio rerio | I51 | GGFGCIYLADT | 1 | Mus musculus | K71 | APCVVKVEPSD | 3 | Homo sapiens, Mus musculus, Bos taurus | K71 | QQMVMKIEPST | 1 | Caenorhabditis elegans | K71 | APYVIKVEPSD | 1 | Danio rerio | L184 | KASNLLLNYKN | 1 | Homo sapiens | L184 | KAANILLEKQG | 1 | Caenorhabditis elegans | L184 | KASNLLLSYTN | 1 | Danio rerio | L184 | KASNLLLSHKN | 1 | Mus musculus | L184 | KASNLLLSYKN | 1 | Bos taurus | M131 | YRFMIMDRFGS | 2 | Homo sapiens, Mus musculus | M131 | MRYMIIPKYAT | 1 | Caenorhabditis elegans | M131 | YRFMVMDRFGT | 1 | Danio rerio | M131 | YRFMIIDRFGS | 1 | Bos taurus | R133 | FMIMDRFGSDL | 2 | Homo sapiens, Mus musculus | R133 | YMIIPKYATSL | 1 | Caenorhabditis elegans | R133 | FMVMDRFGTDL | 1 | Danio rerio | R133 | FMIIDRFGSDL | 1 | Bos taurus | V196 | DQVYLVDYGLA | 3 | Homo sapiens, Mus musculus, Bos taurus | V196 | STAVLVDFGLA | 1 | Caenorhabditis elegans | V196 | NQVFLVDYGLA | 1 | Danio rerio | V69 | SDAPCVVKVEP | 2 | Homo sapiens, Mus musculus | V69 | KSQQMVMKIEP | 1 | Caenorhabditis elegans | V69 | ADAPYVIKVEP | 1 | Danio rerio | V69 | NDAPCVVKVEP | 1 | Bos taurus | Y87 | TELKFYQRAAK | 3 | Homo sapiens, Mus musculus, Bos taurus | Y87 | TEVVVFNRILK | 1 | Caenorhabditis elegans | Y87 | SELKFYMRAAK | 1 | Danio rerio |
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