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

Gene ID: 9860, updated on 2-Nov-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
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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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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
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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

  • 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

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