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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

LRRC1 Gene

protein-coding   GIFtS: 53
GCID: GC06P053706

Leucine Rich Repeat Containing 1

(Previous name: leucine-rich repeat-containing 1)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Leucine Rich Repeat Containing 11 2     LAP And No PDZ Protein2 3
LANO2 3 5     dJ523E19.12
Leucine-Rich Repeat-Containing 11 2     LAP (Leucine-Rich Repeats And PDZ) And No PDZ Protein2
LANO Adapter Protein2 3     Leucine-Rich Repeat-Containing Protein 12

External Ids:    HGNC: 143071   Entrez Gene: 552272   Ensembl: ENSG000001372697   OMIM: 6081955   UniProtKB: Q9BTT63   

Export aliases for LRRC1 gene to outside databases

Previous GC identifers: GC00U990863 GC06P053660 GC06P053767 GC06P053492


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for LRRC1 Gene: 
LRRC1 (leucine rich repeat containing 1) is a protein-coding gene. Diseases associated with LRRC1 include juvenile myoclonic epilepsy, and idiopathic generalized epilepsy. An important paralog of this gene is LRRC7.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NT_007592.15  NC_018917.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the LRRC1 gene promoter:
         Max1   RP58   AML1a   Egr-1   HNF-1A   E47   AREB6   HNF-1   Hlf   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): LRRC1 promoter sequence
   Search SABiosciences Chromatin IP Primers for LRRC1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat LRRC1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p12.1   Ensembl cytogenetic band:  6p12.1   HGNC cytogenetic band: 6p12.2

LRRC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
LRRC1 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P053706:  view genomic region     (about GC identifiers)

Start:
53,659,295 bp from pter      End:
53,788,919 bp from pter
Size:
129,625 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: LRRC1_HUMAN, Q9BTT6 (See protein sequence)
Recommended Name: Leucine-rich repeat-containing protein 1  
Size: 524 amino acids; 59242 Da
Subunit: Interacts with DLG1 and DLG4. May form a complex with DLG1 and ERBB2IP, where interaction between LRRC1
and ERBB2IP is indirect
Subcellular location: Cytoplasm. Membrane; Peripheral membrane protein. Note=Localized at the basolateral side of
epithelial cells
Sequence caution: Sequence=BAA91801.1; Type=Frameshift; Positions=262;
Secondary accessions: Q5TGN3 Q9HAC0 Q9NVF1
Alternative splicing: 2 isoforms:  Q9BTT6-1   Q9BTT6-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for LRRC1: NX_Q9BTT6

Explore proteomics data for LRRC1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9BTT6

  • LRRC1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    LRRC1 Protein Expression
    REFSEQ proteins: NP_060684.4  
    ENSEMBL proteins: 
     ENSP00000435217   ENSP00000359925   ENSP00000359919  

    Human Recombinant Protein Products for LRRC1: 
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    Cloud-Clone Corp. Proteins for LRRC1 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--
    GO:0016020membrane IEA--

    LRRC1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    2 InterPro protein domains:
     IPR001611 Leu-rich_rpt
     IPR025875 Leu-rich_rpt_4

    Graphical View of Domain Structure for InterPro Entry Q9BTT6

    ProtoNet protein and cluster: Q9BTT6

    UniProtKB/Swiss-Prot: LRRC1_HUMAN, Q9BTT6
    Similarity: Contains 17 LRR (leucine-rich) repeats


    LRRC1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
         
    LRRC1 for ontologies           About GeneDecksing


    Phenotypes:
         3 GenomeRNAi human phenotypes for LRRC1:
     Decreased melanin production  G0/1 arrest  Increased G1 DNA content 

    Animal Models:
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    miRTarBase miRNAs that target LRRC1:
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    8/23 QIAGEN miScript miRNA Assays for microRNAs that regulate LRRC1 (see all 23):
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    SwitchGear 3'UTR luciferase reporter plasmidLRRC1 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for LRRC1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

    5/564 Interacting proteins for LRRC1 (Q9BTT62, 3 ENSP000003599254) via UniProtKB, MINT, STRING, and/or I2D (see all 564)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    KIAA1377Q9P2H02, 3MINT-65337 I2D: score=5 
    CRMP1Q141942, 3MINT-65336 I2D: score=4 
    ERBB2IPQ96RT13, ENSP000003703304I2D: score=3 STRING: ENSP00000370330
    SLX4Q8IY923, ENSP000002940084I2D: score=2 STRING: ENSP00000294008
    DLG1Q129593, ENSP000003457314I2D: score=3 STRING: ENSP00000345731
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for LRRC1

    Search CenterWatch for drugs/clinical trials and news about LRRC1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for LRRC1 gene (2 alternative transcripts): 
    NM_025168.1  NM_018214.4  

    Unigene Cluster for LRRC1:

    Leucine rich repeat containing 1
    Hs.606493  [show with all ESTs]
    Unigene Representative Sequence: NM_018214
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000487251 ENST00000370888(uc003pcd.1) ENST00000370882 ENST00000490222

    miRNA
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    8/23 QIAGEN miScript miRNA Assays for microRNAs that regulate LRRC1 (see all 23):
    hsa-miR-142-3p hsa-miR-3910 hsa-miR-3200-5p hsa-miR-300 hsa-miR-199b-3p hsa-miR-199a-3p hsa-miR-3129-5p hsa-miR-124
    SwitchGear 3'UTR luciferase reporter plasmidLRRC1 3' UTR sequence
    Inhib. RNA
    Products:
         
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat LRRC1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat LRRC1

    Additional mRNA sequence: 

    AF332199.1 AF359380.1 AJ420513.1 AK001637.1 AK292248.1 BC003193.1 

    6 DOTS entries:

    DT.409860  DT.95165918  DT.70103763  DT.95206216  DT.121393288  DT.75142061 

    24/109 AceView cDNA sequences (see all 109):

    BC003193 D62624 AA237081 AK021896 BF063416 NM_025168 CA777562 CA777835 
    BU609169 BI828737 AK001637 AW440514 BI765219 D79260 D82313 BQ771831 
    BI832427 AI271631 BM926879 BI764145 AI569940 BE140861 AA428611 AU119761 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for LRRC1    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b
    SP1:                                                  -                                         -     -                                 
    SP2:                                                  -                                                                                 
    SP3:                                                                                                                                    
    SP4:                                                                                                                                    
    SP5:                                                                                                                                    


    ECgene alternative splicing isoforms for LRRC1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    LRRC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCCAATCAGT
    LRRC1 Expression
    About this image


    See LRRC1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for LRRC1

    SOURCE GeneReport for Unigene cluster: Hs.606493

    UniProtKB/Swiss-Prot: LRRC1_HUMAN, Q9BTT6
    Tissue specificity: Expressed strongly in testis and placenta, followed by heart, lung, kidney, thyroid, trachea,
    colon, prostate and pancreas

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for LRRC1 gene from 7/16 species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Lrrc11 , 5 leucine rich repeat containing 11, 5 88.68(n)1
    93.13(a)1
      9 (43.36 cM)5
    2143451  NM_001146048.11  NP_001139520.11 
     774308235 
    chicken
    (Gallus gallus)
    Aves LRRC11 leucine rich repeat containing 1 81.99(n)
    87.87(a)
      421891  XM_419907.3  XP_419907.2 
    lizard
    (Anolis carolinensis)
    Reptilia LRRC16
    leucine rich repeat containing 1
    86(a)
    1 ↔ 1
    GL343342.1(36339-134867)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.152002 Xenopus laevis transcribed sequence with moderate similarity more 76.68(n)    CA791258.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.109552 Transcribed sequence with moderate similarity to protein more 78.19(n)    57069206 
    fruit fly
    (Drosophila melanogaster)
    Insecta scrib6
    scribbled
    11(a)
    1 → many
    3R(22362072-22429773)
    worm
    (Caenorhabditis elegans)
    Secernentea let-4136
    Protein lap1
    29(a)
    1 → many
    V(7972924-7977774)


    ENSEMBL Gene Tree for LRRC1 (if available)
    TreeFam Gene Tree for LRRC1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for LRRC1 gene
    LRRC72  LRRC22  ERBB2IP2  MFHAS12  LRRC302  LRRIQ42  SCRIB2  SHOC22  
    LRRD12  LRRC10B2  LRRC392  LRRC402  LRRC102  
    10 SIMAP similar genes for LRRC1 using alignment to 2 protein entries:     LRRC1_HUMAN (see all proteins):
    SCRIB    ERBB2IP    LRRC7    LRRC8C    LRCH3    LRRD1
    RSU1    LRRC8E    PHLPP1    LRRC28

    LRRC1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/2641 SNPs in LRRC1 are shown (see all 2641)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1822349791,2
    C--53657935(+) GGACAC/GGTCTT 1 -- us2k10--------
    rs2010841921,2
    C--53658026(+) GCCTT-/TTTTTAAT 1 -- us2k10--------
    rs113635701,2
    C--53658031(+) TTTAA-/TTTTTT 1 -- us2k1 tfbs3 trp30--------
    rs773331311,2
    C,F--53658049(+) AAGCAG/TTTGGA 1 -- us2k11Minor allele frequency- T:0.09EA 120
    rs1389225411,2
    C--53658206(+) TCTGTA/GAGAAC 1 -- us2k10--------
    rs38138501,2
    C,F,A,H--53658211(-) CCTGCG/ATTCTC 1 -- us2k123Minor allele frequency- A:0.19NS EA NA CSA WA 2584
    rs1494316351,2
    --53658232(+) GGACAA/CACAAA 1 -- us2k10--------
    rs1447711981,2
    --53658266(+) ACGGAG/TTTTCG 1 -- us2k10--------
    rs1853336531,2
    --53658300(+) GGTGAC/TAATGC 1 -- us2k10--------
    rs1397242461,2
    --53658499(+) ACTTTA/GCCTTG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for LRRC1 (53659295 - 53788919 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for LRRC1:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2667284CNV Deletion23128226
    nsv5306CNV Insertion18451855
    esv5680CNV Gain19470904
    nsv830664CNV Gain17160897

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 608195    OMIM disorders: --

    4 diseases for LRRC1:    About MalaCards
    juvenile myoclonic epilepsy    idiopathic generalized epilepsy    thyroiditis    prostatitis

    1 disease from the University of Copenhagen DISEASES database for LRRC1:
    Idiopathic generalized epilepsy

    LRRC1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): LRRC1

    Export disorders for LRRC1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for LRRC1 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with LRRC1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Identification and mutational analysis of candidate genes for juvenile myoclonic epilepsy on 6p11-p12: LRRC1, GCLC, KIAA0057 and CLIC5. (PubMed id 12200217)1, 2 Suzuki T.... Yamakawa K. (2002)
    4. Lano, a novel LAP protein directly connected to MAGUK proteins in epithelial cells. (PubMed id 11440998)1, 2 Saito H.... Borg J.-P. (2001)
    5. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    6. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (2012)
    7. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    8. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    9. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    10. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 55227 HGNC: 14307 AceView: LRRC1 Ensembl:ENSG00000137269 euGenes: HUgn55227
    ECgene: LRRC1 H-InvDB: LRRC1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for LRRC1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for LRRC1 gene:
    Search GeneIP for patents involving LRRC1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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