LRRK2 (leucine-rich repeat kinase 2)

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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
Donations are also welcome

LRRK2 (leucine-rich repeat kinase 2)

Identity

Other names	AURA17
	DARDARIN
	PARK8
	RIPK7
	ROCO2
HGNC (Hugo)	LRRK2
LocusID (NCBI)	120892
Location	12q12
Location_base_pair	Starts at 40618813 and ends at 40763086 bp from pter ( according to hg19-Feb_2009)
Note	Non-annotated gene. Preliminary data : if you are an author who wish to write a full paper/card on this gene, go to How to contribute

DNA/RNA

External links

	Nomenclature
HGNC (Hugo)	LRRK2 18618
	Cards
Entrez_Gene (NCBI)	LRRK2 120892 leucine-rich repeat kinase 2
GeneCards (Weizmann)	LRRK2
Ensembl hg19 (Hinxton)	ENSG00000188906 [Gene_View] chr12:40618813-40763086 [Contig_View] LRRK2 [Vega]
Ensembl hg38 (Hinxton)	ENSG00000188906 [Gene_View] chr12:40618813-40763086 [Contig_View] LRRK2 [Vega]
ICGC DataPortal	ENSG00000188906
cBioPortal	LRRK2
AceView (NCBI)	LRRK2
Genatlas (Paris)	LRRK2
WikiGenes	120892
SOURCE (Princeton)	LRRK2
	Genomic and cartography
GoldenPath hg19 (UCSC)	LRRK2 - chr12:40618813-40763086 + 12q12 [Description] (hg19-Feb_2009)
GoldenPath hg38 (UCSC)	LRRK2 - 12q12 [Description] (hg38-Dec_2013)
Ensembl	LRRK2 - 12q12 [CytoView hg19] LRRK2 - 12q12 [CytoView hg38]
Mapping of homologs : NCBI	LRRK2 [Mapview hg19] LRRK2 [Mapview hg38]
OMIM	607060 609007
	Gene and transcription
Genbank (Entrez)	AK026776 AK122640 AK127729 AK131537 AL832453
RefSeq transcript (Entrez)	NM_198578
RefSeq genomic (Entrez)	AC_000144 NC_000012 NC_018923 NG_011709 NT_029419 NW_001838057 NW_004929384
Consensus coding sequences : CCDS (NCBI)	LRRK2
Cluster EST : Unigene	Hs.187636 [ NCBI ]
CGAP (NCI)	Hs.187636
Alternative Splicing : Fast-db (Paris)	GSHG0006587
Alternative Splicing Gallery	ENSG00000188906
Gene Expression	LRRK2 [ NCBI-GEO ] LRRK2 [ SEEK ] LRRK2 [ MEM ]
SOURCE (Princeton)	Expression in : [Normal Tissue Atlas] [carcinoma Classsification] [NCI60]
	Protein : pattern, domain, 3D structure
UniProt/SwissProt	Q5S007 (Uniprot)
NextProt	Q5S007 [Medical]
With graphics : InterPro	Q5S007
Splice isoforms : SwissVar	Q5S007 (Swissvar)
Catalytic activity : Enzyme	2.7.11.1 [ Enzyme-Expasy ] 2.7.11.1 2.7.11.1 [ IntEnz-EBI ] 2.7.11.1 [ BRENDA ] 2.7.11.1 [ KEGG ]
Domaine pattern : Prosite (Expaxy)	LRR (PS51450) PROTEIN_KINASE_ATP (PS00107) PROTEIN_KINASE_DOM (PS50011) PROTEIN_KINASE_ST (PS00108) ROC (PS51424)
Domains : Interpro (EBI)	Ankyrin_rpt-contain_dom ARM-like ARM-type_fold Kinase-like_dom Leu-rich_rpt Leu-rich_rpt_4 Leu-rich_rpt_typical-subtyp MIRO-like P-loop_NTPase Prot_kinase_dom Protein_kinase_ATP_BS ROC_GTPase Ser/Thr_kinase_AS Small_GTP-bd_dom Small_GTPase WD40/YVTN_repeat-like_dom WD40_repeat WD40_repeat_dom
Related proteins : CluSTr	Q5S007
Domain families : Pfam (Sanger)	LRR_1 (PF00560) LRR_4 (PF12799) LRR_8 (PF13855) Miro (PF08477) Pkinase (PF00069)
Domain families : Pfam (NCBI)	pfam00560 pfam12799 pfam13855 pfam08477 pfam00069
Domain families : Smart (EMBL)	LRR_TYP (SM00369) WD40 (SM00320)
DMDM Disease mutations	120892
Blocks (Seattle)	Q5S007
PDB (SRS)	2ZEJ 3D6T
PDB (PDBSum)	2ZEJ 3D6T
PDB (IMB)	2ZEJ 3D6T
PDB (RSDB)	2ZEJ 3D6T
Human Protein Atlas	ENSG00000188906
Peptide Atlas	Q5S007
IPI	IPI00175649 IPI00425978 IPI00657922 IPI00794835 IPI00894207
	Protein Interaction databases
DIP (DOE-UCLA)	Q5S007
IntAct (EBI)	Q5S007
FunCoup	ENSG00000188906
BioGRID	LRRK2
IntegromeDB	LRRK2
STRING (EMBL)	LRRK2
	Ontologies - Pathways
QuickGO	Q5S007
Ontology : AmiGO	SNARE binding MAPK cascade activation of MAPKK activity activation of MAPK activity positive regulation of protein phosphorylation glycoprotein binding actin binding GTPase activity protein kinase activity protein serine/threonine kinase activity MAP kinase kinase activity enzyme inhibitor activity GTPase activator activity protein binding ATP binding GTP binding extracellular space cytoplasm mitochondrion mitochondrial outer membrane mitochondrial inner membrane mitochondrial matrix lysosome endosome endoplasmic reticulum Golgi apparatus trans-Golgi network cytosol plasma membrane GTP catabolic process autophagy response to oxidative stress small GTPase mediated signal transduction neuromuscular junction development synaptic vesicle determination of adult lifespan positive regulation of autophagy positive regulation of autophagy regulation of neuron maturation tubulin binding inclusion body kinase activity Rho GTPase binding syntaxin-1 binding peptidyl-serine phosphorylation peptidyl-threonine phosphorylation peptidyl-threonine phosphorylation olfactory bulb development tangential migration from the subventricular zone to the olfactory bulb clathrin binding axon axon dendrite dendrite positive regulation of protein ubiquitination cytoplasmic vesicle mitochondrial membrane negative regulation of protein binding positive regulation of proteasomal ubiquitin-dependent protein catabolic process cytoplasmic side of mitochondrial outer membrane dendrite cytoplasm GTP-dependent protein kinase activity GTP-dependent protein kinase activity negative regulation of GTPase activity regulation of kidney size exploration behavior regulation of locomotion regulation of membrane potential identical protein binding protein homodimerization activity neuron projection neuronal cell body positive regulation of programmed cell death perikaryon perikaryon positive regulation of GTPase activity positive regulation of GTPase activity ion channel binding membrane raft protein autophosphorylation protein autophosphorylation intracellular distribution of mitochondria neuron projection morphogenesis protein kinase A binding regulation of mitochondrial depolarization positive regulation of dopamine receptor signaling pathway regulation of dendritic spine morphogenesis extracellular vesicular exosome neuron death cellular response to organic cyclic compound regulation of neuron death regulation of neuroblast proliferation regulation of synaptic vesicle transport negative regulation of late endosome to lysosome transport negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation regulation of branching morphogenesis of a nerve regulation of synaptic vesicle exocytosis
Ontology : EGO-EBI	SNARE binding MAPK cascade activation of MAPKK activity activation of MAPK activity positive regulation of protein phosphorylation glycoprotein binding actin binding GTPase activity protein kinase activity protein serine/threonine kinase activity MAP kinase kinase activity enzyme inhibitor activity GTPase activator activity protein binding ATP binding GTP binding extracellular space cytoplasm mitochondrion mitochondrial outer membrane mitochondrial inner membrane mitochondrial matrix lysosome endosome endoplasmic reticulum Golgi apparatus trans-Golgi network cytosol plasma membrane GTP catabolic process autophagy response to oxidative stress small GTPase mediated signal transduction neuromuscular junction development synaptic vesicle determination of adult lifespan positive regulation of autophagy positive regulation of autophagy regulation of neuron maturation tubulin binding inclusion body kinase activity Rho GTPase binding syntaxin-1 binding peptidyl-serine phosphorylation peptidyl-threonine phosphorylation peptidyl-threonine phosphorylation olfactory bulb development tangential migration from the subventricular zone to the olfactory bulb clathrin binding axon axon dendrite dendrite positive regulation of protein ubiquitination cytoplasmic vesicle mitochondrial membrane negative regulation of protein binding positive regulation of proteasomal ubiquitin-dependent protein catabolic process cytoplasmic side of mitochondrial outer membrane dendrite cytoplasm GTP-dependent protein kinase activity GTP-dependent protein kinase activity negative regulation of GTPase activity regulation of kidney size exploration behavior regulation of locomotion regulation of membrane potential identical protein binding protein homodimerization activity neuron projection neuronal cell body positive regulation of programmed cell death perikaryon perikaryon positive regulation of GTPase activity positive regulation of GTPase activity ion channel binding membrane raft protein autophosphorylation protein autophosphorylation intracellular distribution of mitochondria neuron projection morphogenesis protein kinase A binding regulation of mitochondrial depolarization positive regulation of dopamine receptor signaling pathway regulation of dendritic spine morphogenesis extracellular vesicular exosome neuron death cellular response to organic cyclic compound regulation of neuron death regulation of neuroblast proliferation regulation of synaptic vesicle transport negative regulation of late endosome to lysosome transport negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation regulation of branching morphogenesis of a nerve regulation of synaptic vesicle exocytosis
Pathways : KEGG	Parkinson's disease
Protein Interaction Database	LRRK2
DoCM (Curated mutations)	LRRK2
Wikipedia pathways	LRRK2
	Gene fusion - rearrangements
	Polymorphisms : SNP, variants
NCBI Variation Viewer	LRRK2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)	LRRK2
dbVar	LRRK2
ClinVar	LRRK2
1000_Genomes	LRRK2
Exome Variant Server	LRRK2
SNP (GeneSNP Utah)	LRRK2
SNP : HGBase	LRRK2
Genetic variants : HAPMAP	LRRK2
Genomic Variants (DGV)	LRRK2 [DGVbeta]
	Mutations
ICGC Data Portal	ENSG00000188906
Somatic Mutations in Cancer : COSMIC	LRRK2
CONAN: Copy Number Analysis	LRRK2
LOVD (Leiden Open Variation Database)	Whole genome datasets
LOVD (Leiden Open Variation Database)	LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)	LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)	MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
LOVD (Leiden Open Variation Database)	Parkinson's disease Mutation Database
Impact of mutations	[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor]
	Diseases
DECIPHER (Syndromes)	12:40618813-40763086
Mutations and Diseases : HGMD	LRRK2
OMIM	607060 609007
Medgen	LRRK2
NextProt	Q5S007 [Medical]
GENETests	LRRK2
Disease Genetic Association	LRRK2
Huge Navigator	LRRK2 [HugePedia] LRRK2 [HugeCancerGEM]
snp3D : Map Gene to Disease	120892
DGIdb (Drug Gene Interaction db)	LRRK2
	General knowledge
Homologs : HomoloGene	LRRK2
Homology/Alignments : Family Browser (UCSC)	LRRK2
Phylogenetic Trees/Animal Genes : TreeFam	LRRK2
Chemical/Protein Interactions : CTD	120892
Chemical/Pharm GKB Gene	PA134968052
Clinical trial	LRRK2
Cancer Resource (Charite)	ENSG00000188906
	Other databases
	Probes
	Litterature
PubMed	499 Pubmed reference(s) in Entrez
CoreMine	LRRK2
GoPubMed	LRRK2
iHOP	LRRK2

Genes in title	automatic search in PubMed
REVIEW articles	automatic search in PubMed
Last year publications	automatic search in PubMed

Search in all EBI NCBI

Contributor(s)

Written	09-2002	Dessen P, Le Minor S

Updated	12-2014	Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology

indexed on : Sat Feb 14 17:25:43 CET 2015

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jlhuret@AtlasGeneticsOncology.org.