mutated Ligand Binding Site gene DataBase





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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 GRIK2
Gene summary
Basic gene Info.Gene symbolGRIK2
Gene nameglutamate receptor, ionotropic, kainate 2
CytomapUCSC genome browser: 6q16.3
Type of geneprotein-coding
DescriptionbA487F5.1excitatory amino acid receptor 4gluR-6glutamate receptor 6glutamate receptor form Aglutamate receptor form Bglutamate receptor form Cglutamate receptor form Dglutamate receptor form Eglutamate receptor ionotropic, kainate 2
Modification date20141207
dbXrefs MIM : 138244
Ensembl : ENSG00000164418
HPRD : 00692
Vega : OTTHUMG00000016328
ProteinUniProt: Q13002
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GRIK2
BioGPS: 2898
PathwayNCI Pathway Interaction Database: GRIK2
Pathway Commons: GRIK2
ContextiHOP: GRIK2
ligand binding site mutation search in PubMed: GRIK2
UCL Cancer Institute: GRIK2
Assigned class in mutLBSgeneDBA: This gene has a literature evidence and it belongs to targetable_mutLBSgenes.
References showing study about ligand binding site mutation for GRIK2.1. "Motazacker MM, Rost BR, Hucho T, Garshasbi M, Kahrizi K, Ullmann R, Abedini SS, Nieh SE, Amini SH, Goswami C, Tzschach A, Jensen LR, Schmitz D, Ropers HH, Najmabadi H, Kuss AW. A defect in the ionotropic glutamate receptor 6 gene (GRIK2) is associated with autosomal recessive mental retardation. Am J Hum Genet. 2007 Oct;81(4):792-8. Epub 2007 Aug 31. PubMed PMID: 17847003; PubMedCentral PMCID: PMC2227928. " 17847003

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0050804regulation of synaptic transmission15537878

Ligand binding site mutations for GRIK2
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 GRIK2
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 GRIK2 from PDB

Differential gene expression and gene-gene network for GRIK2
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 GRIK2 and the right PPI network was created from samples without mutations in the LBS of GRIK2. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for GRIK2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0004352Autistic Disorder10Biomarker, GeneticVariation
umls:C0005586Bipolar Disorder2Biomarker, GeneticVariation
umls:C0033953Sexual Dysfunctions, Psychological1Biomarker
umls:C0236969Substance-Related Disorders1Biomarker

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

Pharmacological information for GRIK2
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.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
NutraceuticalDB00142L-Glutamic AcidSmall molecule
Approved|illicitDB00237ButabarbitalSmall molecule
Approved|illicitDB00241ButalbitalSmall molecule
Approved|illicitDB00306TalbutalSmall molecule
Approved|vet_approvedDB00312PentobarbitalSmall molecule
Approved|vet_approvedDB00418SecobarbitalSmall molecule
WithdrawnDB00463MetharbitalSmall molecule
Approved|vet_approvedDB00599ThiopentalSmall molecule
Approved|vet_approvedDB00794PrimidoneSmall molecule
ApprovedDB00849MethylphenobarbitalSmall molecule
ApprovedDB01174PhenobarbitalSmall molecule
Approved|illicitDB01351AmobarbitalSmall molecule
Approved|illicitDB01352AprobarbitalSmall molecule
Approved|illicitDB01353ButethalSmall molecule
ApprovedDB01354HeptabarbitalSmall molecule
ApprovedDB01355HexobarbitalSmall molecule
IllicitDB01483BarbitalSmall molecule
Experimental|illicitDB01496Barbituric acid derivativeSmall molecule
ExperimentalDB02852Domoic AcidSmall molecule
ExperimentalDB02999QuisqualateSmall molecule
ExperimentalDB034252s,4r-4-MethylglutamateSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of GRIK2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of GRIK2
Multiple alignments for Q13002 in multiple species
LBSAA sequence# speciesSpecies
A518AVAPLAITYVR2Homo sapiens, Rattus norvegicus
A518VVGDIAIVTKR2Arabidopsis thaliana, Arabidopsis thaliana
A518VVGDVAIVTNR1Arabidopsis thaliana
A518GVGDITIITER1Arabidopsis thaliana
A689AVEDGATMTFF2Homo sapiens, Rattus norvegicus
A689--QVGSYAENY1Arabidopsis thaliana
A689--QVGSFAENY1Arabidopsis thaliana
A689--QVGSFAESY1Arabidopsis thaliana
A689--PQGSFVRDY1Arabidopsis thaliana
E440VTTILEEP--Y2Homo sapiens, Rattus norvegicus
E440PGGTSETPRGW1Arabidopsis thaliana
E440PGGTSVTPRGW1Arabidopsis thaliana
E440PGETFTKPRGW1Arabidopsis thaliana
E440PGHSIKIPRGW1Arabidopsis thaliana
E738YAFLMESTTIE2Homo sapiens, Rattus norvegicus
E738-AIVDERPYVD1Arabidopsis thaliana
E738-AIVDERPYID1Arabidopsis thaliana
E738-AIVDERPYVE1Arabidopsis thaliana
E738-AVVDERAYIE1Arabidopsis thaliana
G688GAVEDGATMTF2Homo sapiens, Rattus norvegicus
G688---QVGSYAEN1Arabidopsis thaliana
G688---QVGSFAEN1Arabidopsis thaliana
G688---QVGSFAES1Arabidopsis thaliana
G688---PQGSFVRD1Arabidopsis thaliana
L517LAVAPLAITYV2Homo sapiens, Rattus norvegicus
L517AVVGDIAIVTK2Arabidopsis thaliana, Arabidopsis thaliana
L517GVVGDVAIVTN1Arabidopsis thaliana
L517AGVGDITIITE1Arabidopsis thaliana
M737DYAFLMESTTI2Homo sapiens, Rattus norvegicus
M737--AIVDERPYV2Arabidopsis thaliana, Arabidopsis thaliana
M737--AIVDERPYI1Arabidopsis thaliana
M737--AVVDERAYI1Arabidopsis thaliana
N721VLVKSNEEGIQ2Homo sapiens, Rattus norvegicus
N721AAALQNGT---1Arabidopsis thaliana
N721ANALQNGT---1Arabidopsis thaliana
N721AKALKDGPSKG1Arabidopsis thaliana
N721DKALRDGPGKG1Arabidopsis thaliana
P516DLAVAPLAITY2Homo sapiens, Rattus norvegicus
P516DAVVGDIAIVT2Arabidopsis thaliana, Arabidopsis thaliana
P516DGVVGDVAIVT1Arabidopsis thaliana
P516DAGVGDITIIT1Arabidopsis thaliana
R523AITYVREKVID2Homo sapiens, Rattus norvegicus
R523AIVTKRTRIVD2Arabidopsis thaliana, Arabidopsis thaliana
R523AIVTNRTKIVD1Arabidopsis thaliana
R523TIITERTKMAD1Arabidopsis thaliana
T690VEDGATMTFFK2Homo sapiens, Rattus norvegicus
T690-QVGSYAENYM1Arabidopsis thaliana
T690-QVGSFAENYM1Arabidopsis thaliana
T690-QVGSFAESYL1Arabidopsis thaliana
T690-PQGSFVRDYL1Arabidopsis thaliana
T741LMESTTIEFVT2Homo sapiens, Rattus norvegicus
T741VDERPYVDLFL1Arabidopsis thaliana
T741VDERPYIDLFL1Arabidopsis thaliana
T741VDERPYVELFL1Arabidopsis thaliana
T741VDERAYIELFL1Arabidopsis thaliana
V685IEYGAVEDGAT2Homo sapiens, Rattus norvegicus
V685VGF---QVGSY1Arabidopsis thaliana
V685IGF---QVGSF1Arabidopsis thaliana
V685IGY---QVGSF1Arabidopsis thaliana
V685IGY---PQGSF1Arabidopsis thaliana
Y488VEDGKYGAQDD2Homo sapiens, Rattus norvegicus
Y488V---LFGDGLK1Arabidopsis thaliana
Y488I---FFGDGLT1Arabidopsis thaliana
Y488I---PYGNGKE1Arabidopsis thaliana
Y488V---AFGNGHD1Arabidopsis thaliana

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