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    LRRN1 leucine rich repeat neuronal 1 [ Homo sapiens (human) ]

    Gene ID: 57633, updated on 9-Dec-2024

    Summary

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    Official Symbol
    LRRN1provided by HGNC
    Official Full Name
    leucine rich repeat neuronal 1provided by HGNC
    Primary source
    HGNC:HGNC:20980
    See related
    Ensembl:ENSG00000175928 MIM:619623; AllianceGenome:HGNC:20980
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NLRR1; NLRR-1; FIGLER3
    Summary
    Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be located in membrane. Predicted to be active in extracellular matrix and extracellular space. Biomarker of stomach cancer. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in brain (RPKM 12.5), testis (RPKM 4.5) and 8 other tissues See more
    Orthologs
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    Genomic context

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    See LRRN1 in Genome Data Viewer
    Location:
    3p26.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (3799431..3849834)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (3795791..3845800)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (3841115..3891518)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14009 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:3168955-3169685 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19345 Neighboring gene tRNA nucleotidyl transferase 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:3310572-3310785 Neighboring gene cereblon Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69928 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69934 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69968 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:3600748-3601947 Neighboring gene uncharacterized LOC100130207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14011 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14013 Neighboring gene Sharpr-MPRA regulatory region 107 Neighboring gene uncharacterized LOC102723512 Neighboring gene polyribonucleotide nucleotidyltransferase 1 pseudogene 1 Neighboring gene sulfatase modifying factor 1

    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. Leucine-rich repeat neuronal protein-1 suppresses apoptosis of gastric cancer cells through regulation of Fas/FasL. Liu B, et al. Cancer Sci, 2019 Jul. PMID 31087525, Free PMC Article
    2. Leucine-Rich Repeat Neuronal Protein 1 Regulates Differentiation of Embryonic Stem Cells by Post-Translational Modifications of Pluripotency Factors. Liao CH, et al. Stem Cells, 2018 Oct. PMID 29893054
    3. N-MYC promotes cell proliferation through a direct transactivation of neuronal leucine-rich repeat protein-1 (NLRR1) gene in neuroblastoma. Hossain MS, et al. Oncogene, 2008 Oct 9. PMID 18591937
    4. Whole-genome sequencing identifies variants in ANK1, LRRN1, HAS1, and other genes and regulatory regions for stroke in type 1 diabetes. Antikainen AA, et al. Sci Rep, 2024 Jun 11. PMID 38862513, Free PMC Article
    5. Neuronal leucine-rich repeat 1 negatively regulates anaplastic lymphoma kinase in neuroblastoma. Satoh S, et al. Sci Rep, 2016 Sep 8. PMID 27604320, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Whole-genome sequencing identifies variants in ANK1, LRRN1, HAS1, and other genes and regulatory regions for stroke in type 1 diabetes.
      Title: Whole-genome sequencing identifies variants in ANK1, LRRN1, HAS1, and other genes and regulatory regions for stroke in type 1 diabetes.
    2. Authors found that LRRN1 contributes to pluripotency of hESC by preventing translocation of OCT4, NANOG, and SOX2 from nucleus to cytoplasm, thereby lessening their post-translational modification and degradation.
      Title: Leucine-Rich Repeat Neuronal Protein 1 Regulates Differentiation of Embryonic Stem Cells by Post-Translational Modifications of Pluripotency Factors.
    3. Study found that LRRN1 is upregulated in gastric cancer (GC) tissue samples and its expression is closely related to poor prognosis. Knocking down LRRN1 expression promoted GC cell apoptosis, and activated the Fas/FasL pathway.
      Title: Leucine-rich repeat neuronal protein-1 suppresses apoptosis of gastric cancer cells through regulation of Fas/FasL.
    4. NLRR1 appears to be an extracellular negative regulator of ALK signalling in neuroblastoma and neuronal development.
      Title: Neuronal leucine-rich repeat 1 negatively regulates anaplastic lymphoma kinase in neuroblastoma.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Polymorphisms in leucine-rich repeat genes are associated with autism spectrum disorder susceptibility in populations of European ancestry.
    6. N-MYC promotes cell proliferation through a direct transactivation of neuronal leucine-rich repeat protein-1 (NLRR1) gene in neuroblastoma.
      Title: N-MYC promotes cell proliferation through a direct transactivation of neuronal leucine-rich repeat protein-1 (NLRR1) gene in neuroblastoma.
    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
    Genetics of callous-unemotional behavior in children.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1497

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of synapse assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 1
    Names
    fibronectin type III, immunoglobulin and leucine rich repeat domains 3
    neuronal leucine-rich repeat protein 1

    NCBI Reference Sequences (RefSeq)

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    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_001324188.2 → NP_001311117.1  leucine-rich repeat neuronal protein 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC023484, BC012463
      Consensus CDS
      CCDS33685.1
      UniProtKB/Swiss-Prot
      Q3LID5, Q6UXK5, Q8IYV5, Q9H8V1, Q9P231
      UniProtKB/TrEMBL
      A8K6Q2
      Conserved Domains (8) summary
      smart00082
      Location:371 → 419
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:13 → 273
      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:429 → 516
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:339 → 362
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:97 → 120
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:531 → 600
      fn3; Fibronectin type III domain
      pfam13855
      Location:119 → 179
      LRR_8; Leucine rich repeat
      cl11960
      Location:431 → 516
      Ig; Immunoglobulin domain

    2. NM_001324189.2 → NP_001311118.1  leucine-rich repeat neuronal protein 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC023484, BC012463
      Consensus CDS
      CCDS33685.1
      UniProtKB/Swiss-Prot
      Q3LID5, Q6UXK5, Q8IYV5, Q9H8V1, Q9P231
      UniProtKB/TrEMBL
      A8K6Q2
      Conserved Domains (8) summary
      smart00082
      Location:371 → 419
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:13 → 273
      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:429 → 516
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:339 → 362
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:97 → 120
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:531 → 600
      fn3; Fibronectin type III domain
      pfam13855
      Location:119 → 179
      LRR_8; Leucine rich repeat
      cl11960
      Location:431 → 516
      Ig; Immunoglobulin domain

    3. NM_020873.7 → NP_065924.3  leucine-rich repeat neuronal protein 1 precursor

      See identical proteins and their annotated locations for NP_065924.3

      Status: VALIDATED

      Description
      Transcript Variant: Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC023484, AK291717, AU154359, BC012463, BC034947, BU685265, CX867219, DA736067
      Consensus CDS
      CCDS33685.1
      UniProtKB/Swiss-Prot
      Q3LID5, Q6UXK5, Q8IYV5, Q9H8V1, Q9P231
      UniProtKB/TrEMBL
      A8K6Q2
      Related
      ENSP00000314901.3, ENST00000319331.4
      Conserved Domains (8) summary
      smart00082
      Location:371 → 419
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:13 → 273
      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:429 → 516
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:339 → 362
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:97 → 120
      LRR_RI; leucine-rich repeat [structural motif]
      pfam00041
      Location:531 → 600
      fn3; Fibronectin type III domain
      pfam13855
      Location:119 → 179
      LRR_8; Leucine rich repeat
      cl11960
      Location:431 → 516
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      3799431..3849834
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448644.1 → XP_047304600.1  leucine-rich repeat neuronal protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q3LID5, Q6UXK5, Q8IYV5, Q9H8V1, Q9P231
      UniProtKB/TrEMBL
      A8K6Q2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      3795791..3845800
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347405.1 → XP_054203380.1  leucine-rich repeat neuronal protein 1 isoform X1

      UniProtKB/Swiss-Prot
      Q3LID5, Q6UXK5, Q8IYV5, Q9H8V1, Q9P231
      UniProtKB/TrEMBL
      A8K6Q2
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UXK5.1 GenPept UniProtKB/Swiss-Prot:Q6UXK5

    Gene LinkOut

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

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