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 RND3
Gene summary
Basic gene Info.Gene symbolRND3
Gene nameRho family GTPase 3
SynonymsARHE|Rho8|RhoE|memB
CytomapUCSC genome browser: 2q23.3
Type of geneprotein-coding
RefGenesNM_001254738.1,
NM_005168.4,
Descriptionprotein MemBras homolog gene family, member Erho-related GTP-binding protein Rho8rho-related GTP-binding protein RhoEsmall GTP binding protein Rho8
Modification date20141222
dbXrefs MIM : 602924
HGNC : HGNC
Ensembl : ENSG00000115963
HPRD : 04233
Vega : OTTHUMG00000131859
ProteinUniProt: P61587
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RND3
BioGPS: 390
PathwayNCI Pathway Interaction Database: RND3
KEGG: RND3
REACTOME: RND3
Pathway Commons: RND3
ContextiHOP: RND3
ligand binding site mutation search in PubMed: RND3
UCL Cancer Institute: RND3
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID


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Ligand binding site mutations for RND3
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
G80S81YCOAD1
L139L139MLUAD1
L139R140QLUSC1
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 RND3
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
L139L139M-1.668549
L139R140Q-1.2507218
G80S81Y-0.76215581
(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 RND3 from PDB

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Differential gene expression and gene-gene network for RND3
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 RND3 and the right PPI network was created from samples without mutations in the LBS of RND3. 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 RND3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for RND3
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
ExperimentalDB04137Guanosine-5'-TriphosphateSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RND3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
GTPGTP1m7bAG80 L139
GTPGTP2v55BG80 L139
GTPGTP2v55DG80 L139


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Conservation information for LBS of RND3
Multiple alignments for P61587 in multiple species
LBSAA sequence# speciesSpecies
A179YIECSALQSEN3Homo sapiens, Mus musculus, Rattus norvegicus
A38QCGKTALLHVF3Homo sapiens, Mus musculus, Rattus norvegicus
C34VGDSQCGKTAL3Homo sapiens, Mus musculus, Rattus norvegicus
D138VGCKSDLRTDV3Homo sapiens, Mus musculus, Rattus norvegicus
G35GDSQCGKTALL3Homo sapiens, Mus musculus, Rattus norvegicus
G80LWDTSGSPYYD3Homo sapiens, Mus musculus, Rattus norvegicus
K136LLVGCKSDLRT3Homo sapiens, Mus musculus, Rattus norvegicus
K36DSQCGKTALLH3Homo sapiens, Mus musculus, Rattus norvegicus
L139GCKSDLRTDVS3Homo sapiens, Mus musculus, Rattus norvegicus
L180IECSALQSENS3Homo sapiens, Mus musculus, Rattus norvegicus
P54PENYVPTVFEN3Homo sapiens, Mus musculus, Rattus norvegicus
Q33VVGDSQCGKTA3Homo sapiens, Mus musculus, Rattus norvegicus
S32VVVGDSQCGKT3Homo sapiens, Mus musculus, Rattus norvegicus
T37SQCGKTALLHV3Homo sapiens, Mus musculus, Rattus norvegicus
T55ENYVPTVFENY3Homo sapiens, Mus musculus, Rattus norvegicus
T78LSLWDTSGSPY3Homo sapiens, Mus musculus, Rattus norvegicus
V53FPENYVPTVFE3Homo sapiens, Mus musculus, Rattus norvegicus
Y52CFPENYVPTVF3Homo sapiens, Mus musculus, Rattus norvegicus


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