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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

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