mutLBSgeneDB

mutLBSgeneDB
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 NR1I3
Gene summary
Basic gene Info.Gene symbolNR1I3
Gene namenuclear receptor subfamily 1, group I, member 3
SynonymsCAR|CAR1|MB67
CytomapUCSC genome browser: 1q23.3
Type of geneprotein-coding
RefGenesNM_001077469.2,
NM_001077470.2,NM_001077471.2,NM_001077472.2,NM_001077473.2,
NM_001077474.2,NM_001077475.2,NM_001077476.2,NM_001077477.2,
NM_001077478.2,NM_001077479.2,NM_001077480.2,NM_001077481.2,
NM_001077482.2,NM_005122.4,
Descriptionconstitutive activator of retinoid responseconstitutive active receptorconstitutive active responseconstitutive androstane nuclear receptor variant 2constitutive androstane nuclear receptor variant 3constitutive androstane nuclear receptor variant 4
Modification date20141211
dbXrefs MIM : 603881
HGNC : HGNC
Ensembl : ENSG00000143257
HPRD : 04858
Vega : OTTHUMG00000034347
ProteinUniProt: Q14994
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NR1I3
BioGPS: 9970
PathwayNCI Pathway Interaction Database: NR1I3
KEGG: NR1I3
REACTOME: NR1I3
Pathway Commons: NR1I3
ContextiHOP: NR1I3
ligand binding site mutation search in PubMed: NR1I3
UCL Cancer Institute: NR1I3
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 NR1I3.1. Repo, S., Jyrkkärinne, J., Pulkkinen, J. T., Laatikainen, R., Honkakoski, P., & Johnson, M. S. (2008). Ligand specificity of constitutive androstane receptor as probed by induced-fit docking and mutagenesis. Journal of medicinal chemistry, 51(22), 7119-7131. 18973326

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0045944positive regulation of transcription from RNA polymerase II promoter11114890


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Ligand binding site mutations for NR1I3
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
Y330Y332HCOAD1
R183R183HLUAD1
L346M344KLUAD1
F161F161LOV1
V199E200KSKCM1
M168F167LUCEC1
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 NR1I3
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
R183R183H-0.74487642
M168F167L-0.6043584
Y330Y332H-0.57302627
F161F161L-0.56212116
L346M344K-0.28662641
V199E200K-0.2139385
(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 NR1I3 from PDB

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Differential gene expression and gene-gene network for NR1I3
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 NR1I3 and the right PPI network was created from samples without mutations in the LBS of NR1I3. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for NR1I3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0023903Liver Neoplasms6Biomarker
umls:C0028754Obesity3Biomarker
umls:C0019209Hepatomegaly2Biomarker
umls:C0023904Liver Neoplasms, Experimental2Biomarker
umls:C0011849Diabetes Mellitus1Biomarker
umls:C0860207Drug-Induced Liver Injury1Therapeutic
umls:C0524620Metabolic Syndrome X1Biomarker
umls:C0032927Precancerous Conditions1Biomarker

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

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Pharmacological information for NR1I3
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
NutraceuticalDB01708DehydroepiandrosteroneSmall molecule
ExperimentalDB0188916,17-Androstene-3-OlSmall molecule
ExperimentalDB07557(5BETA)-PREGNANE-3,20-DIONESmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of NR1I3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
CID6-(4-CHLOROPHENYL)IMIDAZO[2,1-B][1,3]THIAZOLE-5-CARBALDEHYDE O-(3,4-DICHLOROBENZYL)OXIME1xvpDF161 M168 V199
IIIPeptide ligand (ARG,HIS,LYS,ILE,LEU,HIS,ARG,LEU,LEU,GLN,GLU,GLY)1xv9BR183
IIIPeptide ligand (GLU,ARG,HIS,LYS,ILE,LEU,HIS,ARG,LEU,LEU,GLN,GLU)1xv9DR183
IIIPeptide ligand (ARG,HIS,LYS,ILE,LEU,HIS,ARG,LEU,LEU,GLN,GLU,GLY)1xvpBR183
IIIPeptide ligand (GLU,ARG,HIS,LYS,ILE,LEU,HIS,ARG,LEU,LEU,GLN,GLU)1xvpDR183


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Conservation information for LBS of NR1I3
Multiple alignments for Q14994 in multiple species
LBSAA sequence# speciesSpecies
D228CYKMEDAVH--2Mus musculus, Rattus norvegicus
D228RYTIEDGARVS1Homo sapiens
D228RYTIEDAARVS1Macaca mulatta
D228RYTIEDGAR--1Pan troglodytes
E349MPLLQEICS3Homo sapiens, Macaca mulatta, Pan troglodytes
E349TPLLGEICS1Mus musculus
E349MPLLGEICS1Rattus norvegicus
F161PLVTHFADINT2Homo sapiens, Pan troglodytes
F161PLLTHFADINT2Mus musculus, Rattus norvegicus
F161PLVTHFADVNT1Macaca mulatta
F247FLELLFHFHGT3Homo sapiens, Macaca mulatta, Pan troglodytes
F247FLESILHFHKN1Mus musculus
F247FLELIIHFHKT1Rattus norvegicus
H203AVEICHIVLNT3Homo sapiens, Macaca mulatta, Pan troglodytes
H203AVEILHISLNT2Mus musculus, Rattus norvegicus
I164THFADINTFMV4Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus
I164THFADVNTFMV1Macaca mulatta
I173MVLQVIKFTKD2Homo sapiens, Pan troglodytes
I173MVQQIIKFTKD2Mus musculus, Rattus norvegicus
I173MVQQVIKFTKD1Macaca mulatta
I187FRSLPIEDQIS3Homo sapiens, Macaca mulatta, Pan troglodytes
I187FRSLTMEDQIS2Mus musculus, Rattus norvegicus
I191PIEDQISLLKG3Homo sapiens, Macaca mulatta, Pan troglodytes
I191TMEDQISLLKG2Mus musculus, Rattus norvegicus
I350PLLQEICS3Homo sapiens, Macaca mulatta, Pan troglodytes
I350PLLGEICS2Mus musculus, Rattus norvegicus
K177VIKFTKDLPVF3Homo sapiens, Macaca mulatta, Pan troglodytes
K177IIKFTKDLPLF2Mus musculus, Rattus norvegicus
K195QISLLKGAAVE5Homo sapiens, Macaca mulatta, Pan troglodytes, Mus musculus, Rattus norvegicus
L170NTFMVLQVIKF2Homo sapiens, Pan troglodytes
L170NTFMVQQIIKF2Mus musculus, Rattus norvegicus
L170NTFMVQQVIKF1Macaca mulatta
L194DQISLLKGAAV5Homo sapiens, Macaca mulatta, Pan troglodytes, Mus musculus, Rattus norvegicus
L206ICHIVLNTTFC3Homo sapiens, Macaca mulatta, Pan troglodytes
L206ILHISLNTTFC2Mus musculus, Rattus norvegicus
L243FQVEFLELLFH3Homo sapiens, Macaca mulatta, Pan troglodytes
L243FQYEFLESILH1Mus musculus
L243FQYEFLELIIH1Rattus norvegicus
L246EFLELLFHFHG3Homo sapiens, Macaca mulatta, Pan troglodytes
L246EFLESILHFHK1Mus musculus
L246EFLELIIHFHK1Rattus norvegicus
L346SAMMPLLQEIC3Homo sapiens, Macaca mulatta, Pan troglodytes
L346SAMTPLLGEIC1Mus musculus
L346SAMMPLLGEIC1Rattus norvegicus
M168DINTFMVLQVI2Homo sapiens, Pan troglodytes
M168DINTFMVQQII2Mus musculus, Rattus norvegicus
M168DVNTFMVQQVI1Macaca mulatta
N165HFADINTFMVL2Homo sapiens, Pan troglodytes
N165HFADINTFMVQ2Mus musculus, Rattus norvegicus
N165HFADVNTFMVQ1Macaca mulatta
Q190LPIEDQISLLK3Homo sapiens, Macaca mulatta, Pan troglodytes
Q190LTMEDQISLLK2Mus musculus, Rattus norvegicus
R183DLPVFRSLPIE3Homo sapiens, Macaca mulatta, Pan troglodytes
R183DLPLFRSLTME2Mus musculus, Rattus norvegicus
S3---MASREDEL3Homo sapiens, Macaca mulatta, Pan troglodytes
S3TLETMASEEEY1Mus musculus
S3TLETMTSEEEY1Rattus norvegicus
T225GPLRYTIEDGA2Homo sapiens, Pan troglodytes
T225GPLCYKMEDAV2Mus musculus, Rattus norvegicus
T225GPLRYTIEDAA1Macaca mulatta
V199LKGAAVEICHI3Homo sapiens, Macaca mulatta, Pan troglodytes
V199LKGAAVEILHI2Mus musculus, Rattus norvegicus
Y224CGPLRYTIEDG2Homo sapiens, Pan troglodytes
Y224CGPLCYKMEDA2Mus musculus, Rattus norvegicus
Y224CGPLRYTIEDA1Macaca mulatta
Y330SINEAYGYQIQ3Homo sapiens, Macaca mulatta, Pan troglodytes
Y330SINNAYSYELQ1Mus musculus
Y330SINSAYSYEIH1Rattus norvegicus


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