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    LILRA2 leukocyte immunoglobulin like receptor A2 [ Homo sapiens (human) ]

    Gene ID: 11027, updated on 28-Oct-2024

    Summary

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    Official Symbol
    LILRA2provided by HGNC
    Official Full Name
    leukocyte immunoglobulin like receptor A2provided by HGNC
    Primary source
    HGNC:HGNC:6603
    See related
    Ensembl:ENSG00000239998 MIM:604812; AllianceGenome:HGNC:6603
    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
    ILT1; LIR7; CD85H; LIR-7
    Summary
    This gene encodes a member of a family of immunoreceptors that are expressed predominantly on monocytes and B cells, and at lower levels on dendritic cells and natural killer cells. The encoded protein is an activating receptor that inhibits dendritic cell differentiation and antigen presentation and suppresses innate immune response. Alternatively spliced transcript variants encoding different isoforms have been found. This gene is located in a cluster of related genes on chromosome 19 and there is a pseudogene for this gene on chromosome 3. [provided by RefSeq, Mar 2014]
    Expression
    Biased expression in bone marrow (RPKM 15.6), spleen (RPKM 8.6) and 5 other tissues See more
    Orthologs
    all
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    Genomic context

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    See LILRA2 in Genome Data Viewer
    Location:
    19q13.42
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54572988..54590287)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57666505..57683802)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (55084455..55101752)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene killer cell immunoglobulin like receptor, three Ig domains X1 (pseudogene) Neighboring gene uncharacterized LOC105372461 Neighboring gene uncharacterized LOC107985347 Neighboring gene leukocyte immunoglobulin like receptor A1 Neighboring gene leukocyte immunoglobulin like receptor B1

    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. Molecular mechanism of the recognition of bacterially cleaved immunoglobulin by the immune regulatory receptor LILRA2. Yamazaki R, et al. J Biol Chem, 2020 Jul 10. PMID 32424043, Free PMC Article
    2. Human myeloid cells express an activating ILT receptor (ILT1) that associates with Fc receptor gamma-chain. Nakajima H, et al. J Immunol, 1999 Jan 1. PMID 9886363
    3. Use of genetic profiling in leprosy to discriminate clinical forms of the disease. Bleharski JR, et al. Science, 2003 Sep 12. PMID 12970564
    4. Down-regulation of leucocyte immunoglobulin-like receptor expression in the synovium of rheumatoid arthritis patients after treatment with disease-modifying anti-rheumatic drugs. Huynh OA, et al. Rheumatology (Oxford), 2007 May. PMID 17202177
    5. Stability engineering, biophysical, and biological characterization of the myeloid activating receptor immunoglobulin-like transcript 1 (ILT1/LIR-7/LILRA2). Chen Y, et al. Protein Expr Purif, 2007 Dec. PMID 17920929

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Overexpression of LILRA2 indicated poor prognosis of ovarian carcinoma: A new potential biomarker and therapeutic target.
      Title: Overexpression of LILRA2 indicated poor prognosis of ovarian carcinoma: A new potential biomarker and therapeutic target.
    2. Molecular mechanism of the recognition of bacterially cleaved immunoglobulin by the immune regulatory receptor LILRA2.
      Title: Molecular mechanism of the recognition of bacterially cleaved immunoglobulin by the immune regulatory receptor LILRA2.
    3. findings demonstrate that LILRA2 is a type of innate immune receptor in the host immune system that detects immunoglobulin abnormalities caused by microbial pathogens.
      Title: Microbially cleaved immunoglobulins are sensed by the innate immune receptor LILRA2.
    4. LILRA2 recognizes microbially cleaved antibodies and activates innate immunity, suggesting that LILRA2 detects dangerous immunological situations in which antibodies are destroyed by pathogens.
      Title: Microbially cleaved immunoglobulins are sensed by the innate immune receptor LILRA2.
    5. LILRA2-mediated activation of monocytes is significantly different to LPS and that LILRA2 selectively modulates LPS-mediated monocyte activation and FcgammaRI-dependent phagocytosis.
      Title: LILRA2 selectively modulates LPS-mediated cytokine production and inhibits phagocytosis by monocytes.
    6. The authors report the LILRA2 extracellular D1D2 domain crystal structure, which reveals structural shifts of the corresponding MHC-binding amino acid residues in comparison with LILR B1/B2, explaining its non-binding to MHC molecules.
      Title: Crystal structure of myeloid cell activating receptor leukocyte Ig-like receptor A2 (LILRA2/ILT1/LIR-7) domain swapped dimer: molecular basis for its non-binding to MHC complexes.
    7. LILRA2 Delta 419-421 isoform encoded by the splice site SNP may play a role in systemic lupus erythematosus and microscopic polyangiitis.
      Title: Association of LILRA2 (ILT1, LIR7) splice site polymorphism with systemic lupus erythematosus and microscopic polyangiitis.
    8. Progenitor mast cells expressed cell surface activating LILRA2. Mature cord-blood-derived mast cells had detectable mRNA encoding multiple LILRs, none were expressed on the cell surface.
      Title: Differential expression of leukocyte immunoglobulin-like receptors on cord-blood-derived human mast cell progenitors and mature mast cells.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Large-scale candidate gene analysis of spontaneous clearance of hepatitis C virus.
    10. LILRA2 activation, by altering GM-CSF-induced monocyte differentiation into immature DC, provides a mechanism for down-regulating the ability of the innate immune system to activate the adaptive T cell response while promoting an inflammatory response.
      Title: LILRA2 activation inhibits dendritic cell differentiation and antigen presentation to T cells.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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

    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

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables IgM binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables antigen binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables inhibitory MHC class I receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables signaling receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in defense response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in immune response-regulating signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in innate immune response activating cell surface receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in interleukin-10-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of lipopolysaccharide-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of toll-like receptor 4 signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in neutrophil activation involved in immune response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of calcium ion transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of cell activation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of granulocyte colony-stimulating factor production IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of granulocyte macrophage colony-stimulating factor production IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of interleukin-1 beta production IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of interleukin-6 production IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of interleukin-6 production IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of interleukin-8 production IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of tumor necrosis factor production IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    leukocyte immunoglobulin-like receptor subfamily A member 2
    Names
    CD85 antigen-like family member H
    immunoglobulin-like transcript 1
    leucocyte Ig-like receptor A2
    leukocyte immunoglobulin-like receptor 7
    leukocyte immunoglobulin-like receptor subfamily A member 2 soluble
    leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 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_034038.2 RefSeqGene

      Range
      5804..22301
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001130917.3 → NP_001124389.2  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform a precursor

      See identical proteins and their annotated locations for NP_001124389.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform a.
      Source sequence(s)
      AC245036, AK310088, CB046242, U82278
      Consensus CDS
      CCDS46179.1
      UniProtKB/Swiss-Prot
      O75020, Q8N149
      UniProtKB/TrEMBL
      A0A0G2JMW8
      Related
      ENSP00000375618.3, ENST00000391738.8
      Conserved Domains (2) summary
      smart00410
      Location:35 → 116
      IG_like; Immunoglobulin like
      cl11960
      Location:27 → 117
      Ig; Immunoglobulin domain

    2. NM_001290270.1 → NP_001277199.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform c precursor

      See identical proteins and their annotated locations for NP_001277199.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks in-frame exons in the 5' and 3' coding regions, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AC245036, AK310088, CB046242, U82276
      Consensus CDS
      CCDS74453.1
      UniProtKB/TrEMBL
      A0A0G2JMW8, A8MZH0
      Related
      ENSP00000375617.1, ENST00000391737.3
      Conserved Domains (2) summary
      smart00410
      Location:23 → 104
      IG_like; Immunoglobulin like
      cl11960
      Location:15 → 105
      Ig; Immunoglobulin domain

    3. NM_001290271.2 → NP_001277200.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform d precursor

      See identical proteins and their annotated locations for NP_001277200.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, and lacks an exon and contains an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (d) has a distinct C-terminus and is longer than isoform a.
      Source sequence(s)
      AC245036, AK310088, CB046242, DA264697
      UniProtKB/TrEMBL
      A0A0G2JMC9
      Conserved Domains (2) summary
      smart00410
      Location:35 → 116
      IG_like; Immunoglobulin like
      cl11960
      Location:122 → 217
      Ig; Immunoglobulin domain

    4. NM_006866.4 → NP_006857.2  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform b precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AC245036, BC027916, CB046242, DA465773, DA931441
      Consensus CDS
      CCDS12900.1
      UniProtKB/TrEMBL
      A0A0G2JMW8
      Related
      ENSP00000251376.3, ENST00000251376.7
      Conserved Domains (2) summary
      smart00410
      Location:35 → 116
      IG_like; Immunoglobulin like
      cl11960
      Location:27 → 117
      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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      54572988..54590287
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438112.1 → XP_047294068.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X1

    2. XM_011526390.2 → XP_011524692.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X2

      UniProtKB/TrEMBL
      E9PDF4
      Related
      ENSP00000388131.1, ENST00000439534.5
      Conserved Domains (2) summary
      smart00410
      Location:35 → 116
      IG_like; Immunoglobulin like
      cl11960
      Location:122 → 217
      Ig; Immunoglobulin domain

    3. XM_011526391.2 → XP_011524693.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X3

      Conserved Domains (2) summary
      smart00410
      Location:35 → 116
      IG_like; Immunoglobulin like
      cl11960
      Location:122 → 217
      Ig; Immunoglobulin domain

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003571054.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      479378..496677
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329647.1 → XP_054185622.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X1

    2. XM_054329648.1 → XP_054185623.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X2

    3. XM_054329649.1 → XP_054185624.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X3

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NW_003571060.1 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      477872..495171
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331474.1 → XP_054187449.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X1

    2. XM_054331475.1 → XP_054187450.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X2

    3. XM_054331476.1 → XP_054187451.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X3

    Reference GRCh38.p14 ALT_REF_LOCI_9

    Genomic

    1. NT_187693.1 Reference GRCh38.p14 ALT_REF_LOCI_9

      Range
      555569..572866
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054333610.1 → XP_054189585.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X1

    2. XM_054333611.1 → XP_054189586.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X2

    3. XM_054333612.1 → XP_054189587.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      57666505..57683802
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319655.1 → XP_054175630.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X1

    2. XM_054319656.1 → XP_054175631.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X2

    3. XM_054319657.1 → XP_054175632.1  leukocyte immunoglobulin-like receptor subfamily A member 2 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N149.3 GenPept UniProtKB/Swiss-Prot:Q8N149

    Gene LinkOut

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

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