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

Gene ID: 11027, updated on 11-Apr-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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Location:
19q13.42
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54572988..54590287)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57666505..57683802)
105.20220307 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
  • 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. Overexpression of LILRA2 indicated poor prognosis of ovarian carcinoma: A new potential biomarker and therapeutic target. Zhang Y, et al. Taiwan J Obstet Gynecol, 2023 Jan. PMID 36720556
  2. 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
  3. Microbially cleaved immunoglobulins are sensed by the innate immune receptor LILRA2. Hirayasu K, et al. Nat Microbiol, 2016 Apr 25. PMID 27572839
  4. LILRA2 selectively modulates LPS-mediated cytokine production and inhibits phagocytosis by monocytes. Lu HK, et al. PLoS One, 2012. PMID 22479404, Free PMC Article
  5. 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. Chen Y, et al. J Mol Biol, 2009 Feb 27. PMID 19230061

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_2023_10

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

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