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 LRRK2
Gene summary
Basic gene Info.Gene symbolLRRK2
Gene nameleucine-rich repeat kinase 2
SynonymsAURA17|DARDARIN|PARK8|RIPK7|ROCO2
CytomapUCSC genome browser: 12q12
Type of geneprotein-coding
RefGenesNM_198578.3,
Descriptionaugmented in rheumatoid arthritis 17leucine-rich repeat serine/threonine-protein kinase 2
Modification date20141222
dbXrefs MIM : 609007
HGNC : HGNC
Ensembl : ENSG00000188906
Vega : OTTHUMG00000059742
ProteinUniProt: Q5S007
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LRRK2
BioGPS: 120892
PathwayNCI Pathway Interaction Database: LRRK2
KEGG: LRRK2
REACTOME: LRRK2
Pathway Commons: LRRK2
ContextiHOP: LRRK2
ligand binding site mutation search in PubMed: LRRK2
UCL Cancer Institute: LRRK2
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0000165MAPK cascade17200152
GO:0000186activation of MAPKK activity19302196
GO:0000187activation of MAPK activity19302196
GO:0006184GTP catabolic process21048939
GO:0010955negative regulation of protein processing21370995
GO:0018105peptidyl-serine phosphorylation19576176
GO:0018107peptidyl-threonine phosphorylation21048939
GO:0031398positive regulation of protein ubiquitination16352719
GO:0032092positive regulation of protein binding21370995
GO:0034260negative regulation of GTPase activity22423108
GO:0043068positive regulation of programmed cell death17200152
GO:0043547positive regulation of GTPase activity17442267
GO:0046777protein autophosphorylation16269541
GO:1902499positive regulation of protein autoubiquitination16352719
GO:1903125negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation21850687
GO:1903215negative regulation of protein targeting to mitochondrion21370995
GO:2000469negative regulation of peroxidase activity21850687


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Ligand binding site mutations for LRRK2
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
H1453G1451DSKCM1
T1491E1493KSKCM1
D1455S1457YUCEC1
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 LRRK2
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
T1491E1493K-0.89636888
D1455S1457Y-0.73739689
H1453G1451D-0.19922154
(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 LRRK2 from PDB

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Differential gene expression and gene-gene network for LRRK2
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 LRRK2 and the right PPI network was created from samples without mutations in the LBS of LRRK2. 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 LRRK2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0030567Parkinson Disease242AlteredExpression, Biomarker, GeneticVariation
umls:C0242422Parkinsonian Disorders74Biomarker, GeneticVariation
umls:C1846862PARKINSON DISEASE 8, AUTOSOMAL DOMINANT10Biomarker, GeneticVariation
umls:C0007134Carcinoma, Renal Cell1Biomarker
umls:C0014175Endometriosis1Biomarker
umls:C0027746Nerve Degeneration1Biomarker

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

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Pharmacological information for LRRK2

Gene-centered drug-gene interaction network
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 LRRK2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
GDPGUANOSINE-5'-DIPHOSPHATE3d6tBH1453 D1455
GDPGUANOSINE-5'-DIPHOSPHATE2zejAH1453 D1455 T1491
GDPGUANOSINE-5'-DIPHOSPHATE2zejBH1453 D1455 T1491


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Conservation information for LBS of LRRK2
Multiple alignments for Q5S007 in multiple species
LBSAA sequence# speciesSpecies


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