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Aliases for LRRK1 Gene

Aliases for LRRK1 Gene

  • Leucine Rich Repeat Kinase 1 2 3 5
  • Leucine-Rich Repeat Serine/Threonine-Protein Kinase 1 3
  • EC 2.7.11.1 4
  • KIAA1790 4
  • RIPK6 3
  • Roco1 3

External Ids for LRRK1 Gene

Previous GeneCards Identifiers for LRRK1 Gene

  • GC15P099297
  • GC15P099380
  • GC15P101459
  • GC15P077581

Summaries for LRRK1 Gene

Entrez Gene Summary for LRRK1 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 bone mineralization and decreased bone resorption. [provided by RefSeq, Jan 2017]

GeneCards Summary for LRRK1 Gene

LRRK1 (Leucine Rich Repeat Kinase 1) is a Protein Coding gene. Diseases associated with LRRK1 include Osteosclerotic Metaphyseal Dysplasia and Parkinson Disease 3, Autosomal Dominant. Gene Ontology (GO) annotations related to this gene include identical protein binding and protein kinase activity. An important paralog of this gene is LRRK2.

Gene Wiki entry for LRRK1 Gene

Additional gene information for LRRK1 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRRK1 Gene

Genomics for LRRK1 Gene

GeneHancer (GH) Regulatory Elements for LRRK1 Gene

Promoters and enhancers for LRRK1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH15I100917 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.1 51 3.4 RB1 SIN3A ZNF2 ZNF48 RAD21 RFX5 ZNF143 BCLAF1 RUNX3 DEK LOC101927751 LRRK1 GC15P100892
GH15I101745 Promoter/Enhancer 1.3 Ensembl dbSUPER 19.7 +827.0 826986 2 HDGF RB1 NFRKB ZNF335 POLR2B POLR3A ZNF143 SMARCA5 ZNF202 ZNF362 LOC100128108 PIR33824 PIR52825 SNRPA1 WASH3P LRRK1 GC15P101730 GC15M101723
GH15I101293 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 10.6 +376.1 376139 4.7 PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B POLR2B SNRPA1 ENSG00000259172 LINS1 LOC100419174 CERS3-AS1 PRKXP1 RNU6-807P WASH3P LRRK1 ENSG00000270127
GH15I101085 Enhancer 1.5 FANTOM5 Ensembl ENCODE 15.9 +170.3 170317 7.4 HDGF MLX ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 ZNF143 ZNF263 ENSG00000259755 LRRK1 CHSY1 GC15M101045 LOC105371026
GH15I100939 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 14.7 +21.8 21847 2.3 HDGF PKNOX1 SMAD1 RB1 ZSCAN4 BACH1 NEUROD1 EBF1 YBX1 POLR2A LRRK1 CERS3-AS1 LOC100419174 LINS1 CHSY1 LOC101927751 PIR34573
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LRRK1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LRRK1 gene promoter:

Genomic Locations for LRRK1 Gene

Genomic Locations for LRRK1 Gene
chr15:100,919,215-101,078,254
(GRCh38/hg38)
Size:
159,040 bases
Orientation:
Plus strand
chr15:101,459,420-101,610,317
(GRCh37/hg19)

Genomic View for LRRK1 Gene

Genes around LRRK1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRK1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRK1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRK1 Gene

Proteins for LRRK1 Gene

  • Protein details for LRRK1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q38SD2-LRRK1_HUMAN
    Recommended name:
    Leucine-rich repeat serine/threonine-protein kinase 1
    Protein Accession:
    Q38SD2
    Secondary Accessions:
    • Q6NVH5
    • Q6NYC0
    • Q6ZNL9
    • Q6ZNM9
    • Q96JN5
    • Q9H5S3

    Protein attributes for LRRK1 Gene

    Size:
    2015 amino acids
    Molecular mass:
    225393 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    • Homodimer.
    SequenceCaution:
    • Sequence=AAY67799.1; Type=Miscellaneous discrepancy; Note=The cDNA contains a duplication of exon 3.; Evidence={ECO:0000305}; Sequence=BAB15547.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC85472.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for LRRK1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRRK1 Gene

Post-translational modifications for LRRK1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LRRK1 Gene

Domains & Families for LRRK1 Gene

Gene Families for LRRK1 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for LRRK1 Gene

Graphical View of Domain Structure for InterPro Entry

Q38SD2

UniProtKB/Swiss-Prot:

LRRK1_HUMAN :
  • Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. ROCO subfamily.
Family:
  • Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family. ROCO subfamily.
genes like me logo Genes that share domains with LRRK1: view

Function for LRRK1 Gene

Molecular function for LRRK1 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + a protein = ADP + a phosphoprotein.
UniProtKB/Swiss-Prot EnzymeRegulation:
Binding of GTP stimulates kinase activity.

Enzyme Numbers (IUBMB) for LRRK1 Gene

Phenotypes From GWAS Catalog for LRRK1 Gene

Gene Ontology (GO) - Molecular Function for LRRK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004672 protein kinase activity IEA --
GO:0004674 protein serine/threonine kinase activity IBA --
GO:0004871 signal transducer activity IBA --
GO:0005515 protein binding IPI 19712061
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with LRRK1: view
genes like me logo Genes that share phenotypes with LRRK1: view

Animal Models for LRRK1 Gene

MGI Knock Outs for LRRK1:

Clone Products

  • Addgene plasmids for LRRK1

No data available for Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for LRRK1 Gene

Localization for LRRK1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRRK1 Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRRK1 gene
Compartment Confidence
mitochondrion 5
cytosol 5
nucleus 2
peroxisome 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LRRK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA --
GO:0005739 mitochondrion IDA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with LRRK1: view

Pathways & Interactions for LRRK1 Gene

SuperPathways for LRRK1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRRK1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006468 protein phosphorylation IEA --
GO:0016310 phosphorylation IEA --
GO:0035556 intracellular signal transduction IBA --
GO:0036035 osteoclast development IEA --
GO:0045453 bone resorption IEA --
genes like me logo Genes that share ontologies with LRRK1: view

No data available for Pathways by source and SIGNOR curated interactions for LRRK1 Gene

Drugs & Compounds for LRRK1 Gene

(4) Drugs for LRRK1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Approved Nutra 0
Manganese Approved Nutra 37
Guanosine triphosphate Experimental Pharma 0
ATP Investigational Nutra Agonist 0

(1) Additional Compounds for LRRK1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with LRRK1: view

Transcripts for LRRK1 Gene

Unigene Clusters for LRRK1 Gene

Leucine-rich repeat kinase 1:
Representative Sequences:

Clone Products

  • Addgene plasmids for LRRK1

Alternative Splicing Database (ASD) splice patterns (SP) for LRRK1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b · 19c ^ 20 ^ 21 ^ 22
SP1: - - -
SP2: - -
SP3: -
SP4: - -

Relevant External Links for LRRK1 Gene

GeneLoc Exon Structure for
LRRK1
ECgene alternative splicing isoforms for
LRRK1

Expression for LRRK1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRRK1 Gene

Protein differential expression in normal tissues from HIPED for LRRK1 Gene

This gene is overexpressed in Lymph node (23.9) and Uterus (19.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LRRK1 Gene



NURSA nuclear receptor signaling pathways regulating expression of LRRK1 Gene:

LRRK1

SOURCE GeneReport for Unigene cluster for LRRK1 Gene:

Hs.407918
genes like me logo Genes that share expression patterns with LRRK1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRK1 Gene

Orthologs for LRRK1 Gene

This gene was present in the common ancestor of animals.

Orthologs for LRRK1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRRK1 33 34
  • 97.82 (n)
dog
(Canis familiaris)
Mammalia LRRK1 33 34
  • 88.46 (n)
cow
(Bos Taurus)
Mammalia LRRK1 33 34
  • 87.06 (n)
mouse
(Mus musculus)
Mammalia Lrrk1 33 16 34
  • 85.37 (n)
rat
(Rattus norvegicus)
Mammalia Lrrk1 33
  • 84.95 (n)
oppossum
(Monodelphis domestica)
Mammalia LRRK1 34
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 81 (a)
OneToMany
-- 34
  • 80 (a)
OneToMany
-- 34
  • 21 (a)
OneToMany
chicken
(Gallus gallus)
Aves LRRK1 33 34
  • 75.03 (n)
lizard
(Anolis carolinensis)
Reptilia LRRK1 34
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrk1 33
  • 67.14 (n)
Str.13362 33
zebrafish
(Danio rerio)
Actinopterygii lrrk1 33
  • 63.15 (n)
LRRK1 (1 of 2) 34
  • 60 (a)
OneToMany
LRRK1 (2 of 2) 34
  • 47 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Lrrk 34
  • 14 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea lrk-1 34
  • 17 (a)
OneToMany
Species where no ortholog for LRRK1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LRRK1 Gene

ENSEMBL:
Gene Tree for LRRK1 (if available)
TreeFam:
Gene Tree for LRRK1 (if available)

Paralogs for LRRK1 Gene

Paralogs for LRRK1 Gene

(6) SIMAP similar genes for LRRK1 Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with LRRK1: view

Variants for LRRK1 Gene

Sequence variations from dbSNP and Humsavar for LRRK1 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs886038213 uncertain-significance, not provided 101,068,738(+) GAGTGGTG/G coding_sequence_variant, frameshift, genic_downstream_transcript_variant
rs1000014572 -- 100,945,870(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000056483 -- 100,995,322(+) C/T genic_upstream_transcript_variant, intron_variant
rs1000063091 -- 100,954,414(+) A/T genic_upstream_transcript_variant, intron_variant
rs1000073821 -- 100,994,299(+) A/T 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LRRK1 Gene

Variant ID Type Subtype PubMed ID
nsv95032 CNV insertion 16902084
nsv94609 CNV deletion 16902084
nsv833109 CNV gain 17160897
nsv570827 CNV loss 21841781
nsv516426 CNV loss 19592680
nsv469824 CNV loss 16826518
nsv457288 CNV loss 19166990
nsv1133220 CNV tandem duplication 24896259
nsv1041172 CNV gain 25217958
esv3637495 CNV loss 21293372
esv3637494 CNV loss 21293372
esv3637492 CNV gain 21293372
esv3637491 CNV gain 21293372
esv3581866 CNV loss 25503493
esv3581864 CNV loss 25503493
esv3552947 CNV deletion 23714750
esv3443757 CNV insertion 20981092
esv34275 CNV gain 17911159
esv33725 CNV gain 17666407
esv33120 CNV loss 17666407
esv2761889 CNV loss 21179565
esv2760062 CNV gain 17122850
esv2750172 CNV deletion 23290073
esv2750171 CNV deletion 23290073
esv2750170 CNV deletion 23290073
esv2668881 CNV deletion 23128226
esv1932382 CNV deletion 18987734
esv1015225 CNV insertion 17803354
dgv762e212 CNV loss 25503493
dgv761e212 CNV loss 25503493

Variation tolerance for LRRK1 Gene

Residual Variation Intolerance Score: 21.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.04; 96.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRK1 Gene

Human Gene Mutation Database (HGMD)
LRRK1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRK1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRK1 Gene

Disorders for LRRK1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for LRRK1 Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search LRRK1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LRRK1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with LRRK1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LRRK1 Gene

Publications for LRRK1 Gene

  1. Variants in the LRRK1 gene and susceptibility to Parkinson's disease in Norway. (PMID: 17324517) Haugarvoll K … Farrer MJ (Neuroscience letters 2007) 3 22 44 58
  2. LRRK1 protein kinase activity is stimulated upon binding of GTP to its Roc domain. (PMID: 16243488) Korr D … Weiss B (Cellular signalling 2006) 3 4 22 58
  3. Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11347906) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 2 3 4 58
  4. Biochemical characterization of highly purified leucine-rich repeat kinases 1 and 2 demonstrates formation of homodimers. (PMID: 22952686) Civiero L … Taymans JM (PloS one 2012) 3 4 58
  5. Heterodimerization of Lrrk1-Lrrk2: Implications for LRRK2-associated Parkinson disease. (PMID: 20144646) Dachsel JC … Farrer MJ (Mechanisms of ageing and development 2010) 3 22 58

Products for LRRK1 Gene

  • Addgene plasmids for LRRK1

Sources for LRRK1 Gene

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