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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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See PILRA in Genome Data Viewer
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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