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    PILRA paired immunoglobin like type 2 receptor alpha [ Homo sapiens (human) ]

    Gene ID: 29992, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PILRAprovided by HGNC
    Official Full Name
    paired immunoglobin like type 2 receptor alphaprovided by HGNC
    Primary source
    HGNC:HGNC:20396
    See related
    Ensembl:ENSG00000085514 MIM:605341; AllianceGenome:HGNC:20396
    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
    FDF03
    Summary
    Cell signaling pathways rely on a dynamic interaction between activating and inhibiting processes. SHP-1-mediated dephosphorylation of protein tyrosine residues is central to the regulation of several cell signaling pathways. Two types of inhibitory receptor superfamily members are immunoreceptor tyrosine-based inhibitory motif (ITIM)-bearing receptors and their non-ITIM-bearing, activating counterparts. Control of cell signaling via SHP-1 is thought to occur through a balance between PILRalpha-mediated inhibition and PILRbeta-mediated activation. These paired immunoglobulin-like receptor genes are located in a tandem head-to-tail orientation on chromosome 7. This particular gene encodes the ITIM-bearing member of the receptor pair, which functions in the inhibitory role. Alternative splicing has been observed at this locus and three variants, each encoding a distinct isoform, are described. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in appendix (RPKM 17.4), spleen (RPKM 11.8) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    7q22.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100371291..100400096)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (101611370..101640173)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (99971110..99997719)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene STAG3L5P-PVRIG2P-PILRB readthrough Neighboring gene microRNA 6840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26359 Neighboring gene paired immunoglobin like type 2 receptor beta Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:99968027-99968778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26361 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:99995395-99995894 Neighboring gene zinc finger CW-type and PWWP domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26362 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26364 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26365 Neighboring gene methylphosphate capping enzyme

    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. PILRA polymorphism modifies the effect of APOE4 and GM17 on Alzheimer's disease risk. Lopatko Lindman K, et al. Sci Rep, 2022 Aug 2. PMID 35918447, Free PMC Article
    2. The PILRA G78R Variant Correlates with Higher HSV-1-Specific IgG Titers in Alzheimer's Disease. Agostini S, et al. Cell Mol Neurobiol, 2019 Nov. PMID 31297637
    3. Whole-exome sequencing of the BDR cohort: evidence to support the role of the PILRA gene in Alzheimer's disease. Patel T, et al. Neuropathol Appl Neurobiol, 2018 Aug. PMID 29181857, Free PMC Article
    4. PILRα binds an unknown receptor expressed primarily on CD56bright and decidual-NK cells and activates NK cell functions. Ophir Y, et al. Oncotarget, 2016 Jul 5. PMID 27029068, Free PMC Article
    5. Structural basis for simultaneous recognition of an O-glycan and its attached peptide of mucin family by immune receptor PILRα. Kuroki K, et al. Proc Natl Acad Sci U S A, 2014 Jun 17. PMID 24889612, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. New candidate SNPs for genetic association with Alzheimer's disease: a linkage disequilibrium analysis for the FCGRIIB and PILRA genes.
      Title: New candidate SNPs for genetic association with Alzheimer's disease: a linkage disequilibrium analysis for the FCGRIIB and PILRA genes.
    2. PILRA polymorphism modifies the effect of APOE4 and GM17 on Alzheimer's disease risk.
      Title: PILRA polymorphism modifies the effect of APOE4 and GM17 on Alzheimer's disease risk.
    3. The CD8alpha-PILRalpha interaction maintains CD8(+) T cell quiescence.
      Title: The CD8α-PILRα interaction maintains CD8(+) T cell quiescence.
    4. Inhibitory Fcgamma Receptor and Paired Immunoglobulin Type 2 Receptor Alpha Genotypes in Alzheimer's Disease.
      Title: Inhibitory Fcγ Receptor and Paired Immunoglobulin Type 2 Receptor Alpha Genotypes in Alzheimer's Disease.
    5. Herpes simplex virus type 1 IgG are increased in Alzheimer's disease patients with the protective R78 PILRA genotype.
      Title: The PILRA G78R Variant Correlates with Higher HSV-1-Specific IgG Titers in Alzheimer's Disease.
    6. Exome-wide burden analysis revealed significant burden of variants in PILRA in patients with late-onset Alzheimer's disease
      Title: Whole-exome sequencing of the BDR cohort: evidence to support the role of the PILRA gene in Alzheimer's disease.
    7. We propose that PILRA G78R protects individuals from Alzheimer's disease risk via reduced inhibitory signaling in microglia and reduced microglial infection during HSV-1 recurrence.
      Title: Paired Immunoglobulin-like Type 2 Receptor Alpha G78R variant alters ligand binding and confers protection to Alzheimer's disease.
    8. Data suggest that, although PILRA exhibits essentially the same recognition of different glycopeptides, slight modifications of linker sugar cause significant changes in a wide area of the binding interface, resulting in a reduction of binding affinity; analogs/fragments of gpb were used in these studies. (PILRA = paired immunoglobin like type 2 receptor alpha; gpb = envelope glycoprotein B, Herpes simplex virus type 1)
      Title: Structural and thermodynamic analyses reveal critical features of glycopeptide recognition by the human PILRα immune cell receptor.
    9. The interaction of NK cells with PILRalpha expressing targets lead to elevated IFNgamma secretion and cytotoxicity. In conclusion, PILRalpha is a novel NK activating ligand which binds and activates an unknown NK receptor expressed on a unique NK cell subset.
      Title: PILRα binds an unknown receptor expressed primarily on CD56bright and decidual-NK cells and activates NK cell functions.
    10. Transcriptome wide association study results identified two novel genes as statistically significantly associated with nonobstructive azoospermia susceptibility: PILRA and ZNF676.
      Title: Transcriptome-wide association study revealed two novel genes associated with nonobstructive azoospermia in a Chinese population.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    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

    Pathways from PubChem

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    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 MHC class I protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within signal transduction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    paired immunoglobulin-like type 2 receptor alpha
    Names
    cell surface receptor FDF03
    inhibitory receptor PILR-alpha

    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_029837.1 RefSeqGene

      Range
      5043..31652
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_013439.3 → NP_038467.2  paired immunoglobulin-like type 2 receptor alpha isoform 1 precursor

      See identical proteins and their annotated locations for NP_038467.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC005071
      Consensus CDS
      CCDS5691.1
      UniProtKB/Swiss-Prot
      Q8NHI1, Q9UKJ1
      Related
      ENSP00000198536.2, ENST00000198536.7
      Conserved Domains (1) summary
      cl11960
      Location:33 → 150
      Ig; Immunoglobulin domain

    2. NM_178272.2 → NP_840056.1  paired immunoglobulin-like type 2 receptor alpha isoform 2 precursor

      See identical proteins and their annotated locations for NP_840056.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a coding exon, compared to variant 1, resulting in a protein (isoform 2) with a missing internal segment, compared to isoform 1. Isoform 2 is thought to be a soluble protein, since it lacks the transmembrane domain found in isoform 1.
      Source sequence(s)
      AC005071
      Consensus CDS
      CCDS5692.1
      UniProtKB/TrEMBL
      C9JJ79
      Related
      ENSP00000340109.2, ENST00000350573.2
      Conserved Domains (2) summary
      smart00410
      Location:38 → 128
      IG_like; Immunoglobulin like
      cl11960
      Location:33 → 150
      Ig; Immunoglobulin domain

    3. NM_178273.2 → NP_840057.1  paired immunoglobulin-like type 2 receptor alpha isoform 3 precursor

      See identical proteins and their annotated locations for NP_840057.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two internal coding exons, compared to variant 1, which causes a frameshift and results in the shortest isoform (3) that has a distinct C-terminus, compared to isoform 1. Isoform 3 is thought to be a soluble protein, since it lacks the transmembrane domain found in isoform 1.
      Source sequence(s)
      AC005071
      Consensus CDS
      CCDS47660.1
      UniProtKB/TrEMBL
      C9JGG1
      Related
      ENSP00000377569.2, ENST00000394000.6
      Conserved Domains (2) summary
      smart00410
      Location:38 → 128
      IG_like; Immunoglobulin like
      cl11960
      Location:33 → 150
      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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      100371291..100400096
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420292.1 → XP_047276248.1  paired immunoglobulin-like type 2 receptor alpha isoform X1

      UniProtKB/Swiss-Prot
      Q8NHI1, Q9UKJ1

    2. XM_047420291.1 → XP_047276247.1  paired immunoglobulin-like type 2 receptor alpha isoform X1

      UniProtKB/Swiss-Prot
      Q8NHI1, Q9UKJ1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      101611370..101640173
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358038.1 → XP_054214013.1  paired immunoglobulin-like type 2 receptor alpha isoform X1

    2. XM_054358037.1 → XP_054214012.1  paired immunoglobulin-like type 2 receptor alpha isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UKJ1.3 GenPept UniProtKB/Swiss-Prot:Q9UKJ1

    Gene LinkOut

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

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