PILRA

paired immunoglobin like type 2 receptor alpha, the group of V-set domain containing

Basic information

Region (hg38): 7:100367530-100400096

Links

ENSG00000085514 ∙ NCBI:29992 ∙ OMIM:605341 ∙ HGNC:20396 ∙ Uniprot:Q9UKJ1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PILRA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PILRA gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			17	3	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	1

Variants in PILRA

This is a list of pathogenic ClinVar variants found in the PILRA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-100374122-C-T		not specified	Uncertain significance (Jan 23, 2024)
7-100374139-T-C		not specified	Uncertain significance (Nov 09, 2024)
7-100374182-G-A		not specified	Likely benign (Nov 08, 2022)
7-100374211-A-G			Benign (Apr 20, 2019)
7-100374213-G-C		not specified	Uncertain significance (Nov 15, 2024)
7-100374265-C-G		not specified	Uncertain significance (Oct 07, 2024)
7-100374313-A-T		not specified	Uncertain significance (Jan 22, 2025)
7-100374403-A-T		not specified	Uncertain significance (Jan 03, 2022)
7-100374421-T-A		not specified	Likely benign (Aug 17, 2021)
7-100389909-G-A		not specified	Uncertain significance (Sep 10, 2024)
7-100390009-A-G		not specified	Uncertain significance (Jan 29, 2024)
7-100397887-C-T		not specified	Uncertain significance (Aug 09, 2021)
7-100399296-C-T		not specified	Uncertain significance (Sep 27, 2022)
7-100399311-A-G		not specified	Uncertain significance (Dec 15, 2022)
7-100399323-A-C		not specified	Uncertain significance (Feb 23, 2023)
7-100399336-T-C		not specified	Likely benign (Nov 13, 2024)
7-100399797-G-A		not specified	Uncertain significance (May 28, 2023)
7-100399797-G-T		not specified	Uncertain significance (May 31, 2023)
7-100399878-G-A		not specified	Uncertain significance (Apr 11, 2023)
7-100399893-G-A		not specified	Uncertain significance (Aug 02, 2021)
7-100399901-G-C		not specified	Uncertain significance (Oct 05, 2023)
7-100399902-G-C		not specified	Uncertain significance (Dec 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PILRA	protein_coding	protein_coding	ENST00000198536	7	32567

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.73e-11	0.0319	125560	1	187	125748	0.000748

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.446	153	169	0.903	0.00000982	1937
Missense in Polyphen		43	45.957	0.93566		569
Synonymous	-1.32	82	68.1	1.20	0.00000385	636
Loss of Function	-0.226	16	15.1	1.06	8.09e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000358	0.000358
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000370	0.000370
European (Non-Finnish)	0.00121	0.00121
Middle Eastern	0.00	0.00
South Asian	0.00105	0.00101
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Paired receptors consist of highly related activating and inhibitory receptors and are widely involved in the regulation of the immune system. PILRA is thought to act as a cellular signaling inhibitory receptor by recruiting cytoplasmic phosphatases like PTPN6/SHP-1 and PTPN11/SHP-2 via their SH2 domains that block signal transduction through dephosphorylation of signaling molecules. Receptor for PIANP. {ECO:0000269|PubMed:10903717, ECO:0000269|PubMed:21241660}.
• Pathway: Herpes simplex infection - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Intolerance Scores

• loftool: 0.961
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.1

Haploinsufficiency Scores

• pHI: 0.0558
• hipred: N
• hipred_score: 0.327
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.587

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pilra
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: signal transduction;viral process;regulation of immune response
• Cellular component: plasma membrane;integral component of membrane;extracellular exosome
• Molecular function: protein binding;MHC class I protein binding