PVRIG

PVR related immunoglobulin domain containing

Basic information

Region (hg38): 7:100218241-100221490

Links

ENSG00000213413 ∙ NCBI:79037 ∙ OMIM:617012 ∙ HGNC:32190 ∙ Uniprot:Q6DKI7 ∙ 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 PVRIG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PVRIG 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			22	4		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	4	0

Variants in PVRIG

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

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

Position	Type	Phenotype	Significance	ClinVar
7-100219936-C-T		not specified	Uncertain significance (Jan 09, 2023)
7-100219975-G-C		not specified	Uncertain significance (Oct 20, 2023)
7-100219980-C-T		not specified	Uncertain significance (Jun 17, 2024)
7-100219981-G-A		not specified	Uncertain significance (Aug 02, 2021)
7-100220014-T-C		not specified	Uncertain significance (Dec 22, 2023)
7-100220149-G-A		not specified	Uncertain significance (Oct 12, 2021)
7-100220162-C-T		not specified	Uncertain significance (Sep 27, 2021)
7-100220177-G-A		not specified	Likely benign (Mar 22, 2023)
7-100220237-A-G		not specified	Uncertain significance (Jan 09, 2024)
7-100220288-G-A		not specified	Likely benign (Feb 28, 2023)
7-100220300-C-G		not specified	Uncertain significance (Jun 24, 2022)
7-100220381-A-C		not specified	Uncertain significance (Jan 10, 2022)
7-100220447-C-T		not specified	Likely benign (Feb 28, 2023)
7-100220556-C-T		not specified	Uncertain significance (Apr 28, 2022)
7-100220559-C-T		not specified	Uncertain significance (Jun 29, 2022)
7-100220582-C-T		not specified	Uncertain significance (Sep 01, 2021)
7-100220636-G-T		not specified	Uncertain significance (Feb 17, 2022)
7-100220658-G-A		not specified	Uncertain significance (Jan 03, 2022)
7-100220661-G-A		not specified	Uncertain significance (May 26, 2023)
7-100220762-C-T		not specified	Uncertain significance (Oct 05, 2023)
7-100220785-C-T		not specified	Uncertain significance (Jun 05, 2024)
7-100220793-C-G		not specified	Uncertain significance (Feb 09, 2023)
7-100220804-C-T		not specified	Likely benign (Mar 25, 2024)
7-100220986-G-A		not specified	Uncertain significance (Jul 19, 2023)
7-100220991-C-T		not specified	Likely benign (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PVRIG	protein_coding	protein_coding	ENST00000317271	5	3250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00407	0.871	125671	0	53	125724	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0439	210	208	1.01	0.0000133	2005
Missense in Polyphen		92	105.82	0.86937		1214
Synonymous	-2.18	110	84.5	1.30	0.00000523	740
Loss of Function	1.29	5	9.25	0.541	4.82e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000274	0.000243
Ashkenazi Jewish	0.000209	0.000199
East Asian	0.00102	0.000870
Finnish	0.00	0.00
European (Non-Finnish)	0.000241	0.000220
Middle Eastern	0.00102	0.000870
South Asian	0.000178	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface receptor for NECTIN2. May act as a coinhibitory receptor that suppresses T-cell receptor-mediated signals. Following interaction with NECTIN2, inhibits T-cell proliferation. Competes with CD226 for NECTIN2-binding. {ECO:0000269|PubMed:26755705}.

Intolerance Scores

• loftool: 0.681
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.99

Haploinsufficiency Scores

• pHI: 0.0643
• hipred: N
• hipred_score: 0.123
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.257

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pvrig

Gene ontology

• Biological process: negative regulation of T cell receptor signaling pathway
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding;phosphatase binding;signaling receptor activity