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    LRRN2 leucine rich repeat neuronal 2 [ Homo sapiens (human) ]

    Gene ID: 10446, updated on 5-Mar-2024

    Summary

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    Official Symbol
    LRRN2provided by HGNC
    Official Full Name
    leucine rich repeat neuronal 2provided by HGNC
    Primary source
    HGNC:HGNC:16914
    See related
    Ensembl:ENSG00000170382 MIM:605492; AllianceGenome:HGNC:16914
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GAC1; LRRN5; LRANK1; FIGLER7
    Summary
    The protein encoded by this gene belongs to the leucine-rich repeat superfamily. This gene was found to be amplified and overexpressed in malignant gliomas. The encoded protein has homology with other proteins that function as cell-adhesion molecules or as signal transduction receptors and is a candidate for the target gene in the 1q32.1 amplicon in malignant gliomas. Two alternatively spliced transcript variants encoding the same protein have been described for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in brain (RPKM 5.5), kidney (RPKM 2.6) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRRN2 in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (204617170..204685738, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (203881574..203950138, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (204586298..204654866, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene penta-EF-hand domain containing 1 pseudogene Neighboring gene MDM4 regulator of p53 Neighboring gene uncharacterized LOC105371692 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:204541896-204542596 Neighboring gene RNA, 5S ribosomal pseudogene 74 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:204547373-204547904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:204568422-204568952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:204568953-204569483 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:204587827-204588686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:204588687-204589545 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:204606107-204606644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:204606645-204607181 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:204616628-204617298 Neighboring gene uncharacterized LOC124904490 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:204630451-204630952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:204632786-204633286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:204633287-204633787 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:204647222-204647722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:204647723-204648223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:204661677-204662630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:204662631-204663582 Neighboring gene uncharacterized LOC105371693 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:204678087-204679056 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:204679057-204680026 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:204680027-204680996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:204680997-204681964 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:204683914-204684551 Neighboring gene RNA, 5S ribosomal pseudogene 75

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Up-regulated LRRN2 expression as a marker for graft quality in living donor liver transplantation. Tomiyama T, et al. Hepatol Commun, 2022 Oct. PMID 35894759, Free PMC Article
    2. Unfavorable neuroblastoma prognostic factor NLRR2 inhibits cell differentiation by transcriptional induction through JNK pathway. Sheikh A, et al. Cancer Sci, 2016 Sep. PMID 27357360, Free PMC Article
    3. GAC1, a new member of the leucine-rich repeat superfamily on chromosome band 1q32.1, is amplified and overexpressed in malignant gliomas. Almeida A, et al. Oncogene, 1998 Jun 11. PMID 9662332
    4. Prognostic signatures and potential pathogenesis of eRNAs-related genes in colon adenocarcinoma. Rong H, et al. Mol Carcinog, 2022 Jan. PMID 34622496
    5. GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Rietveld CA, et al. Science, 2013 Jun 21. PMID 23722424, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Up-regulated LRRN2 expression as a marker for graft quality in living donor liver transplantation.
      Title: Up-regulated LRRN2 expression as a marker for graft quality in living donor liver transplantation.
    2. Prognostic signatures and potential pathogenesis of eRNAs-related genes in colon adenocarcinoma.
      Title: Prognostic signatures and potential pathogenesis of eRNAs-related genes in colon adenocarcinoma.
    3. NLRR2 must be an inducible gene regulated by the JNK pathway to enhance cell survival and inhibit NB cell differentiation.
      Title: Unfavorable neuroblastoma prognostic factor NLRR2 inhibits cell differentiation by transcriptional induction through JNK pathway.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    EBI GWAS Catalog
    Genome-wide association studies identify four ER negative-specific breast cancer risk loci.
    EBI GWAS Catalog
    GWAS of 126,559 individuals identifies genetic variants associated with educational attainment.
    EBI GWAS Catalog
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables signaling receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat neuronal protein 2
    Names
    fibronectin type III, immunoglobulin and leucine rich repeat domain 7
    glioma amplified on chromosome 1 protein
    leucine rich and ankyrin repeats 1
    leucine rich repeat neuronal 5
    leucine-rich repeat neuronal protein 5

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_006338.3 → NP_006329.2  leucine-rich repeat neuronal protein 2 precursor

      See identical proteins and their annotated locations for NP_006329.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 2. Variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AF030435, AL161793, AL512306, BC034047, T08293
      Consensus CDS
      CCDS1448.1
      UniProtKB/Swiss-Prot
      B2R624, O75325, Q5T0Y0, Q6UXM0, Q8N182
      Related
      ENSP00000356144.3, ENST00000367176.7
      Conserved Domains (7) summary
      cd00116
      Location:62 → 288
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      pfam07679
      Location:430 → 514
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:337 → 360
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:95 → 118
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:117 → 177
      LRR_8; Leucine rich repeat
      cl11960
      Location:438 → 514
      Ig; Immunoglobulin domain
      cl15307
      Location:369 → 412
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    2. NM_201630.2 → NP_963924.1  leucine-rich repeat neuronal protein 2 precursor

      See identical proteins and their annotated locations for NP_963924.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AF030435, AL161793, AL512306, BC034047
      Consensus CDS
      CCDS1448.1
      UniProtKB/Swiss-Prot
      B2R624, O75325, Q5T0Y0, Q6UXM0, Q8N182
      Related
      ENSP00000356145.3, ENST00000367177.4
      Conserved Domains (7) summary
      cd00116
      Location:62 → 288
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      pfam07679
      Location:430 → 514
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:337 → 360
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:95 → 118
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:117 → 177
      LRR_8; Leucine rich repeat
      cl11960
      Location:438 → 514
      Ig; Immunoglobulin domain
      cl15307
      Location:369 → 412
      TPKR_C2; Tyrosine-protein kinase receptor C2 Ig-like domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      204617170..204685738 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      203881574..203950138 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75325.2 GenPept UniProtKB/Swiss-Prot:O75325

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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