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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	79705
Gene name	Leucine rich repeat kinase 1
Gene symbol	LRRK1
Synonyms (NCBI Gene)	OSMDRIPK6Roco1
Chromosome	15
Chromosome location	15q26.3
Summary	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

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

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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

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

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Osteosclerotic metaphyseal dysplasia	Pathogenic	rs2141168796, rs2141653795, rs1258583719, rs886038213, rs766875506	RCV001794939 RCV001794940 RCV002227891 RCV001795385 RCV000625749	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (17)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ANDROGENETIC ALOPECIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANTI-NMDA RECEPTOR ENCEPHALITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DUPUYTREN CONTRACTURE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
KERATOCONUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LRRK1-related disorder	Benign; Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OLIGODENDROGLIOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pancreatic adenocarcinoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYSTEMIC LUPUS ERYTHEMATOSUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TREATMENT-RESISTANT HYPERTENSION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (20)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Autoimmune Diseases of the Nervous System	Autoimmune nervous system disorder	Pubtator	34584012	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Bone Diseases	Bone Disease	BEFREE	28326224		★★★★★ ★☆☆☆☆ Found in Text Mining only
Bone Diseases	Bone disease	Pubtator	36040231, 37857821	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Essential Tremor	Tremor	BEFREE	29812962		★★★★★ ★☆☆☆☆ Found in Text Mining only
Infantile malignant osteopetrosis	Malignant Osteopetrosis	BEFREE	30136304		★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	30558617	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	30039155	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteopetrosis	Osteopetrosis	Pubtator	32119750	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	BEFREE	28326224		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteoporosis	Osteoporosis	Pubtator	32972350	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
OSTEOSCLEROTIC METAPHYSEAL DYSPLASIA	Osteosclerotic Metaphyseal Dysplasia	BEFREE	27055475, 27829680, 31571209		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
OSTEOSCLEROTIC METAPHYSEAL DYSPLASIA	Osteosclerotic Metaphyseal Dysplasia	ORPHANET_DG	27829680		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Osteosclerotic metaphyseal dysplasia	Osteosclerotic Metaphyseal Dysplasia	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
OSTEOSCLEROTIC METAPHYSEAL DYSPLASIA	Osteosclerotic Metaphyseal Dysplasia	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Parkinson Disease	Parkinson disease	BEFREE	16243488, 17225181, 17324517, 17394548, 20144646, 24241507, 29812962, 30039155		★★★★★ ★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	LHGDN	16243488, 17225181, 17324517		★★★★★ ★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	Pubtator	20144646, 24241507, 24947832, 37857821	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Parkinson Disease Secondary	Secondary parkinson disease	Pubtator	20144646	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
PARKINSON DISEASE, LATE-ONSET	Parkinson disease	BEFREE	17324517		★★★★★ ★☆☆☆☆ Found in Text Mining only
Parkinsonian Disorders	Parkinson Disease	BEFREE	17324517, 20144646		★★★★★ ★☆☆☆☆ Found in Text Mining only

LRRK1 (leucine rich repeat kinase 1)