Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	79705
Gene name Gene Name - the full gene name approved by the HGNC.	Leucine rich repeat kinase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	LRRK1
Synonyms (NCBI Gene) Gene synonyms aliases	OSMD, RIPK6, Roco1
Chromosome Chromosome number	15
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	15q26.3
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a multi-domain protein that is a leucine-rich repeat kinase and a GDP/GTP binding protein. The encoded protein is thought to play a role in the regulation of bone mass. Mice lacking a similar gene showed severe osteopetrosis, increased b

Show/Hide all(1)

SNP ID	Visualize variation	Clinical significance	Consequence
rs766875506	G>A,C,T	Pathogenic	Missense variant, non coding transcript variant, stop gained, coding sequence variant

Show/Hide all(21)

miRTarBase ID	miRNA	Experiments
MIRT1120920	hsa-miR-1291	CLIP-seq
MIRT1120921	hsa-miR-1538	CLIP-seq
MIRT1120922	hsa-miR-3173-5p	CLIP-seq
MIRT1120923	hsa-miR-3607-3p	CLIP-seq
MIRT1120924	hsa-miR-4283	CLIP-seq
MIRT1120925	hsa-miR-4292	CLIP-seq
MIRT1120926	hsa-miR-4308	CLIP-seq
MIRT1120927	hsa-miR-4476	CLIP-seq
MIRT1120928	hsa-miR-4489	CLIP-seq
MIRT1120929	hsa-miR-4493	CLIP-seq
MIRT1120930	hsa-miR-4675	CLIP-seq
MIRT1120931	hsa-miR-4741	CLIP-seq
MIRT1120932	hsa-miR-4745-3p	CLIP-seq
MIRT1120933	hsa-miR-4747-3p	CLIP-seq
MIRT1120934	hsa-miR-670	CLIP-seq
MIRT2034232	hsa-miR-146a	CLIP-seq
MIRT2034233	hsa-miR-146b-5p	CLIP-seq
MIRT2034234	hsa-miR-4267	CLIP-seq
MIRT2034235	hsa-miR-4668-3p	CLIP-seq
MIRT2264680	hsa-miR-1275	CLIP-seq
MIRT2264681	hsa-miR-4665-5p	CLIP-seq

Show/Hide all(23)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004672	Function	Protein kinase activity	IEA
GO:0004674	Function	Protein serine/threonine kinase activity	IBA
GO:0004674	Function	Protein serine/threonine kinase activity	IEA
GO:0005515	Function	Protein binding	IPI	19712061, 20144646, 20697350, 24510904, 24947832, 26192437, 32814053
GO:0005524	Function	ATP binding	IEA
GO:0005525	Function	GTP binding	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	IDA
GO:0005829	Component	Cytosol	IDA
GO:0005886	Component	Plasma membrane	IEA
GO:0009967	Process	Positive regulation of signal transduction	IEA
GO:0016020	Component	Membrane	IEA
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0035556	Process	Intracellular signal transduction	IEA
GO:0036035	Process	Osteoclast development	IEA
GO:0042802	Function	Identical protein binding	IPI	19712061, 22952686
GO:0045453	Process	Bone resorption	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0090263	Process	Positive regulation of canonical Wnt signaling pathway	IGI	22899650
GO:0106310	Function	Protein serine kinase activity	IEA
GO:1902533	Process	Positive regulation of intracellular signal transduction	IEA

MIM	HGNC	e!Ensembl
610986	18608	ENSG00000154237

Protein

UniProt ID

Q38SD2

Protein name

Leucine-rich repeat serine/threonine-protein kinase 1 (EC 2.7.11.1)

Protein function

Serine/threonine-protein kinase which phosphorylates RAB proteins involved in intracellular trafficking (PubMed:36040231). Phosphorylates RAB7A; this activity is dependent on protein kinase C (PKC) activation (PubMed:36040231, PubMed:37558661, P

PDB

8E04 , 8E05 , 8E06 , 8FAC

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF08477	Roc	640 → 761		Domain
PF16095	COR	844 → 1046	C-terminal of Roc, COR, domain	Family
PF00069	Pkinase	1243 → 1521	Protein kinase domain	Domain

Sequence

MAGMSQRPPSMYWCVGPEESAVCPERAMETLNGAGDTGGKPSTRGGDPAARSRRTEGIRA
AYRRGDRGGARDLLEEACDQCASQLEKGQLLSIPAAYGDLEMVRYLLSKRLVELPTEPTD
DNPAVVAAYFGHTAVVQELLESLPGPCSPQRLLNWMLALACQRGHLGVVKLLVLTHGADP
ESYAVRKNEFPVIVRLPLYAAIKSGNEDIAIFLLRHGAYFCSYILLDSPDPSKHLLRKYF
IEASPLPSSYPGKTALRVKWSHLRLPWVDLDWLIDISCQITELDLSANCLATLPSVIPWG
LINLRKLNLSDNHLGELPGVQSSDEIICSRLLEIDISSNKLSHLPPGFLHLSKLQKLTAS
KNCLEKLFEEENATNWIGLRKLQELDISDNKLTELPALFLHSFKSLNSLNVSRNNLKVFP
DPWACPLKCCKASRNALECLPDKMAVFWKNHLKDVDFSENALKEVPLGLFQLDALMFLRL
QGNQLAALPPQEKWTCRQLKTLDLSRNQLGKNEDGLKTKRIAFFTTRGRQRSGTEAASVL
EFPAFLSESLEVLCLNDNHLDTVPPSVCLLKSLSELYLGNNPGLRELPPELGQLGNLWQL
DTEDLTISNVPAEIQKEGPKAMLSYLRAQLRKAEKCKLMKMIIVGPPRQGKSTLLEILQT
GRAPQVVHGEATIRTTKWELQRPAGSRAKVESVEFNVWDIGGPASMATVNQCFFTDKALY
VVVWNLALGEEAVANLQFWLLNIEAKAPNAVVLVVGTHLDLIEAKFRVERIATLRAYVLA
LCRSPSGSRATGFPDITFKHLHEISCKSLEGQEGLRQLIFHVTCSMKDVGSTIGCQRLAG
RLIPRSYLSLQEAVLAEQQRRSRDDDVQYLTDRQLEQLVEQTPDNDIKDYEDLQSAISFL
IETGTLLHFPDTSHGLRNLYFLDPIWLSECLQRIFNIKGSRSVAKNGVIRAEDLRMLLVG
TGFTQQTEEQYFQFLAKFEIALPVANDSYLLPHLLPSKPGLDTHGMRHPTANTIQRVFKM
SFVPVGFWQRFIARMLISLAEMDLQLFENKKNTKSRNRKVTIYSFTGNQRNRCSTFRVKR
NQTIYWQEGLLVTFDGGYLSVESSDVNWKKKKSGGMKIVCQSEVRDFSAMAFITDHVNSL
IDQWFPALTATESDGTPLMEQYVPCPVCETAWAQHTDPSEKSEDVQYFDMEDCVLTAIER
DFISCPRHPDLPVPLQELVPELFMTDFPARLFLENSKLEHSEDEGSVLGQGGSGTVIYRA
RYQGQPVAVKRFHIKKFKNFANVPADTMLRHLRATDAMKNFSEFRQEASMLHALQHPCIV
ALIGISIHPLCFALELAPLSSLNTVLSENARDSSFIPLGHMLTQKIAYQIASGLAYLHKK
NIIFCDLKSDNILVWSLDVKEHINIKLSDYGISRQSFHEGALGVEGTPGYQAPEIRPRIV
YDEKVDMFSYGMVLYELLSGQRPALGHHQLQIAKKLSKGIRPVLGQPEEVQFRRLQALMM
ECWDTKPEKRPLALSVVSQMKDPTFATFMYELCCGKQTAFFSSQGQEYTVVFWDGKEESR
NYTVVNTEKGLMEVQRMCCPGMKVSCQLQVQRSLWTATEDQKIYIYTLKGMCPLNTPQQA
LDTPAVVTCFLAVPVIKKNSYLVLAGLADGLVAVFPVVRGTPKDSCSYLCSHTANRSKFS
IADEDARQNPYPVKAMEVVNSGSEVWYSNGPGLLVIDCASLEICRRLEPYMAPSMVTSVV
CSSEGRGEEVVWCLDDKANSLVMYHSTTYQLCARYFCGVPSPLRDMFPVRPLDTEPPAAS
HTANPKVPEGDSIADVSIMYSEELGTQILIHQESLTDYCSMSSYSSSPPRQAARSPSSLP
SSPASSSSVPFSTDCEDSDMLHTPGAASDRSEHDLTPMDGETFSQHLQAVKILAVRDLIW
VPRRGGDVIVIGLEKDSGAQRGRVIAVLKARELTPHGVLVDAAVVAKDTVVCTFENENTE
WCLAVWRGWGAREFDIFYQSYEELGRLEACTRKRR

Sequence length

2015

Interactions

View interactions

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Osteosclerotic Metaphyseal Dysplasia	osteosclerotic metaphyseal dysplasia	rs886038213, rs766875506	N/A

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Crohn Disease	Crohn's disease	N/A	N/A	GWAS
Oligodendroglioma	Oligodendroglioma	N/A	N/A	GWAS
Systemic lupus erythematosus	Systemic lupus erythematosus	N/A	N/A	GWAS

Show/Hide Text Mining Associations (17)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Anti N Methyl D Aspartate Receptor Encephalitis	Associate	34584012
Autoimmune Diseases of the Nervous System	Associate	34584012
Bisphosphonate Associated Osteonecrosis of the Jaw	Associate	32119750, 37920250
Bone Diseases	Associate	36040231, 37857821
Cell Transformation Viral	Associate	20697350
Leukemia Myeloid Acute	Associate	30558617
Leukemic Infiltration	Associate	30558617
Neurodegenerative Diseases	Associate	30039155
Optic Nerve Hypoplasia	Associate	37920250
Osteopetrosis	Associate	32119750
Osteoporosis	Associate	32972350
Osteoporotic Fractures	Associate	32972350
Parkinson Disease	Associate	20144646, 24241507, 24947832, 37857821
Parkinson Disease Secondary	Associate	20144646
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	32242897
Pyle disease	Associate	32119750, 36040231, 37920250
Tooth Resorption	Associate	32119750

LRRK1 (leucine rich repeat kinase 1)