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    LRIG2 leucine rich repeats and immunoglobulin like domains 2 [ Homo sapiens (human) ]

    Gene ID: 9860, updated on 28-Oct-2024

    Summary

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    Official Symbol
    LRIG2provided by HGNC
    Official Full Name
    leucine rich repeats and immunoglobulin like domains 2provided by HGNC
    Primary source
    HGNC:HGNC:20889
    See related
    Ensembl:ENSG00000198799 MIM:608869; AllianceGenome:HGNC:20889
    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
    LIG2; UFS2; LIG-2
    Summary
    This gene encodes a transmembrane protein containing leucine-rich repeats and immunoglobulin-like domains. The encoded protein promotes epidermal growth factor signalling, resulting in increased proliferation. Its expression in the cytoplasm of glioma cells is correlated with poor survival. Mutations in this gene can cause urofacial syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
    Expression
    Ubiquitous expression in thyroid (RPKM 2.7), ovary (RPKM 2.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRIG2 in Genome Data Viewer
    Location:
    1p13.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (113073198..113132260)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (113085129..113144193)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (113615820..113674882)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985189 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:113538968-113539144 Neighboring gene VISTA enhancer hs1672 Neighboring gene LRIG2 divergent transcript Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:113568308-113569055 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:113569056-113569802 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:113569803-113570550 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:113570551-113571296 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:113584341-113585260 Neighboring gene Sharpr-MPRA regulatory region 8666 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:113586182-113587101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1524 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:113615599-113616132 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:113616133-113616664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1527 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7885 Neighboring gene ring finger protein, LIM domain interacting pseudogene 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:113701114-113701959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1530 Neighboring gene ribosomal protein S19 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1531 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:113741139-113741644 Neighboring gene uncharacterized LOC643441 Neighboring gene ribosomal protein S15 pseudogene 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 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. A SINE-VNTR-Alu at the LRIG2 locus is associated with proximal and distal gene expression in CRISPR and population models. Hall A, et al. Sci Rep, 2024 Jan 8. PMID 38191889, Free PMC Article
    2. Characterization and tissue-specific expression of human LRIG2. Holmlund C, et al. Gene, 2004 May 12. PMID 15145052
    3. LRIG and cancer prognosis. Lindquist D, et al. Acta Oncol, 2014 Sep. PMID 25180912, Free PMC Article
    4. LRIG2 expression and prognosis in non-small cell lung cancer. Wang G, et al. Oncol Lett, 2014 Aug. PMID 25013483, Free PMC Article
    5. The transmembrane protein LRIG2 increases tumor progression in skin carcinogenesis. Hoesl C, et al. Mol Oncol, 2019 Nov. PMID 31580518, Free PMC Article

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A SINE-VNTR-Alu at the LRIG2 locus is associated with proximal and distal gene expression in CRISPR and population models.
      Title: A SINE-VNTR-Alu at the LRIG2 locus is associated with proximal and distal gene expression in CRISPR and population models.
    2. LRIG2 regulates cell proliferation, migration and apoptosis of osteosarcoma.
      Title: LRIG2 regulates cell proliferation, migration and apoptosis of osteosarcoma.
    3. Prognostic significance of LRIG2 and LRIG3 proteins in urothelial bladder carcinoma.
      Title: Prognostic significance of LRIG2 and LRIG3 proteins in urothelial bladder carcinoma.
    4. Targeting LRIG2 overcomes resistance to EGFR inhibitor in glioblastoma by modulating GAS6/AXL/SRC signaling.
      Title: Targeting LRIG2 overcomes resistance to EGFR inhibitor in glioblastoma by modulating GAS6/AXL/SRC signaling.
    5. LRIG proteins regulate lipid metabolism via BMP signaling and affect the risk of type 2 diabetes.
      Title: LRIG proteins regulate lipid metabolism via BMP signaling and affect the risk of type 2 diabetes.
    6. A SINE-VNTR-Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus.
      Title: A SINE-VNTR-Alu in the LRIG2 Promoter Is Associated with Gene Expression at the Locus.
    7. epidermal LRIG2 excess is associated with activated EGFR/ERBB4-MAPK signaling and accelerated tumor progression.
      Title: The transmembrane protein LRIG2 increases tumor progression in skin carcinogenesis.
    8. Study discovered novel homozygous missense LRIG2 variants that were predicted to be pathogenic in 2 individuals with non-syndromic bladder outlet obstruction. These observations provide evidence that a peripheral neuropathy is central to the pathobiology of functional bladder outlet obstruction in urofacial syndrome and emphasize the importance of LRIG2 and heparanase 2 for nerve patterning in the urinary tract.
      Title: Lrig2 and Hpse2, mutated in urofacial syndrome, pattern nerves in the urinary bladder.
    9. LRIG2 was identified as the downstream target of miR-149-5p and its expression was regulated by LINC00461/miR-149-5p axis.
      Title: Long non-coding RNA LINC00461/miR-149-5p/LRIG2 axis regulates hepatocellular carcinoma progression.
    10. Study demonstrated that LRIG2 promoted the PDGFRBinduced proliferation of glioblastoma multiforme cells in vitro and in vivo through regulating the PDGFRB signalingmediated cell cycle progression.
      Title: LRIG2 promotes the proliferation and cell cycle progression of glioblastoma cells in vitro and in vivo through enhancing PDGFRβ signaling.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    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

    Associated conditions

    Description Tests
    Urofacial syndrome 2
    MedGen: C3554520 OMIM: 615112 GeneReviews: Urofacial Syndrome
    		Compare labs

    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

    Clone Names

    • KIAA0806, DKFZp451C181

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in innervation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in membrane protein ectodomain proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of axon regeneration IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of membrane protein ectodomain proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of protein localization to cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization to cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of neuron migration IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of platelet-derived growth factor receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 growth cone IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeats and immunoglobulin-like domains protein 2

    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.

    Genomic

    1. NG_042819.2 RefSeqGene

      Range
      5002..64064
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001312686.2 → NP_001299615.1  leucine-rich repeats and immunoglobulin-like domains protein 2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 5' region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AB018349, AL357055, CR936669, DA506094
      UniProtKB/Swiss-Prot
      O94898
      Conserved Domains (7) summary
      cd05763
      Location:516 → 590
      Ig_1; Subgroup of the immunoglobulin (Ig) superfamily
      TIGR00864
      Location:313 → 390
      PCC; polycystin cation channel protein
      COG4886
      Location:46 → 342
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      pfam07679
      Location:593 → 680
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:19 → 42
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:43 → 65
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13927
      Location:394 → 481
      Ig_3; Immunoglobulin domain

    2. NM_014813.3 → NP_055628.1  leucine-rich repeats and immunoglobulin-like domains protein 2 isoform 1 precursor

      See identical proteins and their annotated locations for NP_055628.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK291031, AL357055, CR936669
      Consensus CDS
      CCDS30808.1
      UniProtKB/Swiss-Prot
      O94898, Q9NSN2
      Related
      ENSP00000355396.4, ENST00000361127.6
      Conserved Domains (9) summary
      cd05763
      Location:619 → 693
      Ig_1; Subgroup of the immunoglobulin (Ig) superfamily
      smart00082
      Location:445 → 493
      LRRCT; Leucine rich repeat C-terminal domain
      smart00409
      Location:504 → 598
      IG; Immunoglobulin
      cd00116
      Location:46 → 205
      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:602 → 692
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:122 → 145
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:146 → 168
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:312 → 371
      LRR_8; Leucine rich repeat
      cl11960
      Location:714 → 783
      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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      113073198..113132260
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005271369.3 → XP_005271426.1  leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X3

      Conserved Domains (8) summary
      cd05763
      Location:512 → 586
      Ig_1; Subgroup of the immunoglobulin (Ig) superfamily
      smart00082
      Location:445 → 492
      LRRCT; Leucine rich repeat C-terminal domain
      cd00116
      Location:46 → 205
      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:495 → 585
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:122 → 145
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:146 → 168
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:312 → 371
      LRR_8; Leucine rich repeat
      cl11960
      Location:607 → 676
      Ig; Immunoglobulin domain

    2. XM_024451227.2 → XP_024306995.1  leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X2

      Conserved Domains (7) summary
      cd05763
      Location:516 → 590
      Ig_1; Subgroup of the immunoglobulin (Ig) superfamily
      TIGR00864
      Location:313 → 390
      PCC; polycystin cation channel protein
      COG4886
      Location:46 → 342
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      pfam07679
      Location:593 → 680
      I-set; Immunoglobulin I-set domain
      sd00031
      Location:19 → 42
      LRR_1; leucine-rich repeat [structural motif]
      sd00033
      Location:43 → 65
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13927
      Location:394 → 481
      Ig_3; Immunoglobulin domain

    3. XM_047435521.1 → XP_047291477.1  leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      113085129..113144193
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339874.1 → XP_054195849.1  leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X3

    2. XM_054339873.1 → XP_054195848.1  leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X2

    3. XM_054339872.1 → XP_054195847.1  leucine-rich repeats and immunoglobulin-like domains protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O94898.3 GenPept UniProtKB/Swiss-Prot:O94898

    Gene LinkOut

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

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