mutLBSgeneDB |
Gene summary for LRRK2 |
Gene summary |
Basic gene Info. | Gene symbol | LRRK2 |
Gene name | leucine-rich repeat kinase 2 | |
Synonyms | AURA17|DARDARIN|PARK8|RIPK7|ROCO2 | |
Cytomap | UCSC genome browser: 12q12 | |
Type of gene | protein-coding | |
RefGenes | NM_198578.3, | |
Description | augmented in rheumatoid arthritis 17leucine-rich repeat serine/threonine-protein kinase 2 | |
Modification date | 20141222 | |
dbXrefs | MIM : 609007 | |
HGNC : HGNC | ||
Ensembl : ENSG00000188906 | ||
Vega : OTTHUMG00000059742 | ||
Protein | UniProt: Q5S007 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LRRK2 | |
BioGPS: 120892 | ||
Pathway | NCI Pathway Interaction Database: LRRK2 | |
KEGG: LRRK2 | ||
REACTOME: LRRK2 | ||
Pathway Commons: LRRK2 | ||
Context | iHOP: LRRK2 | |
ligand binding site mutation search in PubMed: LRRK2 | ||
UCL Cancer Institute: LRRK2 | ||
Assigned class in mutLBSgeneDB | B: This gene belongs to targetable_mutLBSgenes. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO Term | PubMed ID | GO:0000165 | MAPK cascade | 17200152 | GO:0000186 | activation of MAPKK activity | 19302196 | GO:0000187 | activation of MAPK activity | 19302196 | GO:0006184 | GTP catabolic process | 21048939 | GO:0010955 | negative regulation of protein processing | 21370995 | GO:0018105 | peptidyl-serine phosphorylation | 19576176 | GO:0018107 | peptidyl-threonine phosphorylation | 21048939 | GO:0031398 | positive regulation of protein ubiquitination | 16352719 | GO:0032092 | positive regulation of protein binding | 21370995 | GO:0034260 | negative regulation of GTPase activity | 22423108 | GO:0043068 | positive regulation of programmed cell death | 17200152 | GO:0043547 | positive regulation of GTPase activity | 17442267 | GO:0046777 | protein autophosphorylation | 16269541 | GO:1902499 | positive regulation of protein autoubiquitination | 16352719 | GO:1903125 | negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation | 21850687 | GO:1903215 | negative regulation of protein targeting to mitochondrion | 21370995 | GO:2000469 | negative regulation of peroxidase activity | 21850687 |
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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 |
LBS | AAchange of nsSNV | Cancer type | # samples | H1453 | G1451D | SKCM | 1 | T1491 | E1493K | SKCM | 1 | D1455 | S1457Y | 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 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. |
LBS | AAchange of nsSNV | Relative stability change | T1491 | E1493K | -0.89636888 | D1455 | S1457Y | -0.73739689 | H1453 | G1451D | -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) |
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Phenotype information for LRRK2 |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C0030567 | Parkinson Disease | 242 | AlteredExpression, Biomarker, GeneticVariation |
umls:C0242422 | Parkinsonian Disorders | 74 | Biomarker, GeneticVariation |
umls:C1846862 | PARKINSON DISEASE 8, AUTOSOMAL DOMINANT | 10 | Biomarker, GeneticVariation |
umls:C0007134 | Carcinoma, Renal Cell | 1 | Biomarker |
umls:C0014175 | Endometriosis | 1 | Biomarker |
umls:C0027746 | Nerve Degeneration | 1 | Biomarker |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for LRRK2 |
Gene-centered drug-gene interaction network |
Drug information targeting mutLBSgene (Approved drugs only) |
Drug status | DrugBank ID | Name | Type | Drug structure |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of LRRK2 go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | GDP | GUANOSINE-5'-DIPHOSPHATE | 3d6t | B | H1453 D1455 | GDP | GUANOSINE-5'-DIPHOSPHATE | 2zej | A | H1453 D1455 T1491 | GDP | GUANOSINE-5'-DIPHOSPHATE | 2zej | B | H1453 D1455 T1491 |
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Conservation information for LBS of LRRK2 |
Multiple alignments for Q5S007 in multiple species |
LBS | AA sequence | # species | Species |
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