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    LILRA3 leukocyte immunoglobulin like receptor A3 [ Homo sapiens (human) ]

    Gene ID: 11026, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LILRA3provided by HGNC
    Official Full Name
    leukocyte immunoglobulin like receptor A3provided by HGNC
    Primary source
    HGNC:HGNC:6604
    See related
    MIM:604818; AllianceGenome:HGNC:6604
    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
    HM31; HM43; ILT6; LIR4; CD85E; ILT-6; LIR-4
    Summary
    This gene encodes a member of a family of immunoreceptors that are expressed predominantly in monocytes and B cells, and at lower levels in dendritic cells and natural killer cells. The encoded protein lacks the transmembrane region found in other members of this family. It acts as a soluble receptor for class I major histocompatibility complex (MHC) antigens. Alternatively spliced transcript variants encoding different isoforms have been found. This gene is located in a cluster of related genes on chromosome 19 and is polymorphic in human populations, with many individuals containing a deletion of this genomic region. [provided by RefSeq, Mar 2014]
    Annotation information
    Annotation category: only annotated on alternate loci in reference assembly
    Orthologs
    all
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    Genomic context

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    See LILRA3 in Genome Data Viewer
    Location:
    19q13.4
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 (ALT_REF_LOCI_9) NT_187693.1 (270964..275379, complement)
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 (ALT_REF_LOCI_1) NW_003571054.1 (270735..275150, complement)
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 (ALT_REF_LOCI_2) NW_003571055.2 (270616..275031, complement)
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 (ALT_REF_LOCI_8) NW_003571061.2 (270991..275406, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57378386..57382801, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 (PATCHES) NW_003571054.1 (270735..275150, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 (PATCHES) NW_003571055.1 (270615..275030, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 (PATCHES) NW_003571061.1 (270990..275405, complement)

    NW_003571054.1Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54778410-54779374 Neighboring gene leukocyte immunoglobulin like receptor B2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:54782879-54784078 Neighboring gene microRNA 4752 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:54803747-54804946 Neighboring gene MPRA-validated peak3552 silencer Neighboring gene leukocyte immunoglobulin like receptor A5 Neighboring gene vomeronasal 1 receptor 104 pseudogene

    NW_003571055.2Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905378 Neighboring gene leukocyte immunoglobulin-like receptor subfamily B member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54720754-54721590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54721591-54722426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54789309-54789810 Neighboring gene microRNA 4752 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:54803747-54804946 Neighboring gene MPRA-validated peak3552 silencer Neighboring gene leukocyte immunoglobulin like receptor A5 Neighboring gene vomeronasal 1 receptor 104 pseudogene

    NW_003571061.2Genomic Context describing neighboring genes Neighboring gene leukocyte immunoglobulin like receptor B2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:54782879-54784078 Neighboring gene microRNA 4752 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:54803747-54804946 Neighboring gene leukocyte immunoglobulin like receptor A5 Neighboring gene vomeronasal 1 receptor 104 pseudogene

    NT_187693.1Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54778410-54779374 Neighboring gene leukocyte immunoglobulin like receptor B2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:54782879-54784078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:54789309-54789810 Neighboring gene microRNA 4752 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:54803747-54804946 Neighboring gene MPRA-validated peak3552 silencer Neighboring gene leukocyte immunoglobulin like receptor A5 Neighboring gene vomeronasal 1 receptor 104 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. LILRA3 deletion is a genetic risk factor of HIV infection. Ahrenstorf G, et al. AIDS, 2017 Jan 2. PMID 27755104
    2. Glycosylation in a mammalian expression system is critical for the production of functionally active leukocyte immunoglobulin-like receptor A3 protein. Lee TH, et al. J Biol Chem, 2013 Nov 15. PMID 24085305, Free PMC Article
    3. Association of the LILRA3 deletion with B-NHL and functional characterization of the immunostimulatory molecule. Low HZ, et al. PLoS One, 2013. PMID 24363809, Free PMC Article
    4. Contribution of functional LILRA3, but not nonfunctional LILRA3, to sex bias in susceptibility and severity of anti-citrullinated protein antibody-positive rheumatoid arthritis. Du Y, et al. Arthritis Rheumatol, 2014 Apr. PMID 24757135
    5. LILRA3 is associated with benign prostatic hyperplasia risk in a Chinese Population. Jiao Y, et al. Int J Mol Sci, 2013 Apr 24. PMID 23615473, Free PMC Article

    See all (56) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Leukocyte Ig-like receptor A3 facilitates inflammation, migration and invasion of synovial tissue-derived fibroblasts via ERK/JNK activation.
      Title: Leukocyte Ig-like receptor A3 facilitates inflammation, migration and invasion of synovial tissue-derived fibroblasts via ERK/JNK activation.
    2. Leukocyte immunoglobulin-like receptor A3 gene deletion in five Chinese populations and protective association with nasopharyngeal carcinoma.
      Title: Leukocyte immunoglobulin-like receptor A3 gene deletion in five Chinese populations and protective association with nasopharyngeal carcinoma.
    3. Soluble LILRA3 is aberrantly expressed in antiphospholipid syndrome (APS) and is a potential marker of thrombotic APS.
      Title: Soluble LILRA3 is aberrantly expressed in antiphospholipid syndrome (APS) and is a potential marker of thrombotic APS.
    4. A susceptibility locus in the IL12B but not LILRA3 region is associated with vascular damage in Takayasu arteritis.
      Title: A susceptibility locus in the IL12B but not LILRA3 region is associated with vascular damage in Takayasu arteritis.
    5. Leukocyte immunoglobulin-like receptor A3 is increased in IBD patients and functions as an anti-inflammatory modulator.
      Title: Leukocyte immunoglobulin-like receptor A3 is increased in IBD patients and functions as an anti-inflammatory modulator.
    6. Association of the Leukocyte Immunoglobulin-like Receptor A3 Gene With Neutrophil Activation and Disease Susceptibility in Adult-Onset Still's Disease.
      Title: Association of the Leukocyte Immunoglobulin-like Receptor A3 Gene With Neutrophil Activation and Disease Susceptibility in Adult-Onset Still's Disease.
    7. in systemic lupus erythematosus serum level elevated and correlated with disease activity and severity
      Title: The expression and clinical significance of different forms of LILRA3 in systemic lupus erythematosus.
    8. Study found possible protective effect of the T allele of LILRB1 rs1061680:T>C and no association with insertion/deletion polymorphisms of LILRA3 with ankylosing spondylitis (AS)
      Title: The effect of LILRB1 but not LILRA3 gene polymorphism in immunopathology of ankylosing spondylitis-A parallel to KIR genes.
    9. LILRA3 polymorphism is associated with Takayasu arteritis.
      Title: Genetic determinants and an epistasis of LILRA3 and HLA-B*52 in Takayasu arteritis.
    10. Mutations in the genes glucokinase regulatory protein (GCKR), RNase L (RNASEL), leukocyte immunoglobulin-like receptor 3 (LILRA3), and dynein axonemal heavy chain 10 (DNAH10) segregated with elevated HDLc levels in families, while no mutations associated with low HDLc.
      Title: Identification of four novel genes contributing to familial elevated plasma HDL cholesterol in humans.
    Submit: New GeneRIF Correction See all GeneRIFs (32)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables inhibitory MHC class I receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in immune response-regulating signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in interleukin-10-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in ficolin-1-rich granule membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in specific granule membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in tertiary granule membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    leukocyte immunoglobulin-like receptor subfamily A member 3
    Names
    CD85 antigen-like family member E
    immunoglobulin-like transcript 6
    leucocyte Ig-like receptor A3
    leukocyte immunoglobulin-like receptor 4
    leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3
    monocyte inhibitory receptor HM43/HM31

    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_034046.1 RefSeqGene

      Range
      5001..9416
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001172654.2 → NP_001166125.1  leukocyte immunoglobulin-like receptor subfamily A member 3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001166125.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AF014924, AI655471, BX280714
      UniProtKB/TrEMBL
      H2B4M3
      Conserved Domains (3) summary
      cd05751
      Location:27 → 119
      Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
      smart00410
      Location:271 → 333
      IG_like; Immunoglobulin like
      cl11960
      Location:261 → 355
      Ig; Immunoglobulin domain

    2. NM_006865.5 → NP_006856.3  leukocyte immunoglobulin-like receptor subfamily A member 3 isoform 1 precursor

      See identical proteins and their annotated locations for NP_006856.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      CU457734
      UniProtKB/Swiss-Prot
      J3KPM2, O15469, O15470, O75016, Q8N151, Q8N154, Q8N6C8, Q8NHJ1, Q8NHJ2, Q8NHJ3, Q8NHJ4
      UniProtKB/TrEMBL
      H2B4M3
      Conserved Domains (3) summary
      cd05751
      Location:27 → 119
      Ig1_LILRB1_like; First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILR)B1 (also known as LIR-1) and similar proteins
      smart00410
      Location:335 → 397
      IG_like; Immunoglobulin like
      cl11960
      Location:124 → 219
      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 ALT_REF_LOCI_1

    Genomic

    1. NW_003571054.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      270735..275150 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NW_003571055.2 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      270616..275031 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_8

    Genomic

    1. NW_003571061.2 Reference GRCh38.p14 ALT_REF_LOCI_8

      Range
      270991..275406 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_9

    Genomic

    1. NT_187693.1 Reference GRCh38.p14 ALT_REF_LOCI_9

      Range
      270964..275379 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      57378386..57382801 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N6C8.3 GenPept UniProtKB/Swiss-Prot:Q8N6C8

    Gene LinkOut

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

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