PVR

PVR cell adhesion molecule, the group of V-set domain containing|CD molecules|C2-set domain containing|Nectins and nectin-like molecules

Basic information

Region (hg38): 19:44643798-44666162

Previous symbols: [ "PVS" ]

Links

ENSG00000073008 ∙ NCBI:5817 ∙ OMIM:173850 ∙ HGNC:9705 ∙ Uniprot:P15151 ∙ 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 PVR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PVR 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				4	2	6
missense			28	3	3	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	28	7	6

Variants in PVR

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

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

Position	Type	Phenotype	Significance	ClinVar
19-44644096-C-T		PVR-related disorder	Benign (Feb 14, 2020)
19-44644152-T-C		not specified	Uncertain significance (Mar 04, 2024)
19-44647231-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-44647322-A-G		not specified	Uncertain significance (Nov 07, 2023)
19-44647342-G-A		PVR-related disorder	Benign (Aug 01, 2019)
19-44647349-A-G		not specified	Uncertain significance (Jun 18, 2021)
19-44647349-A-T		not specified	Uncertain significance (Jul 12, 2022)
19-44647372-G-T		not specified	Uncertain significance (Oct 06, 2022)
19-44647446-G-A		PVR-related disorder	Likely benign (Apr 01, 2019)
19-44647486-G-C		not specified	Uncertain significance (Jan 29, 2024)
19-44647491-G-A		PVR-related disorder	Benign (Apr 01, 2019)
19-44647519-G-A		not specified	Uncertain significance (Mar 20, 2024)
19-44649860-C-G		not specified	Uncertain significance (Aug 04, 2023)
19-44649870-G-A		not specified	Uncertain significance (Oct 03, 2022)
19-44649897-C-T		PVR-related disorder	Likely benign (Dec 16, 2019)
19-44649920-A-G		not specified	Likely benign (Dec 14, 2021)
19-44649934-G-A		not specified	Uncertain significance (May 31, 2022)
19-44649947-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-44650027-G-A		not specified	Uncertain significance (Dec 27, 2023)
19-44650054-C-G		not specified	Uncertain significance (Mar 20, 2023)
19-44650057-G-A		PVR-related disorder	Benign (Mar 13, 2019)
19-44650064-T-C		not specified	Uncertain significance (Jul 15, 2021)
19-44650098-C-T		PVR-related disorder	Benign/Likely benign (Apr 01, 2023)
19-44653915-C-T		not specified	Uncertain significance (May 04, 2022)
19-44653963-C-T		not specified	Uncertain significance (Mar 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PVR	protein_coding	protein_coding	ENST00000425690	8	19753

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.92e-10	0.187	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.999	209	254	0.823	0.0000159	2641
Missense in Polyphen		54	73.871	0.731		810
Synonymous	1.90	87	113	0.772	0.00000768	890
Loss of Function	0.573	16	18.7	0.857	9.77e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000546	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000109	0.000105
Middle Eastern	0.000546	0.000544
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates NK cell adhesion and triggers NK cell effector functions. Binds two different NK cell receptors: CD96 and CD226. These interactions accumulates at the cell-cell contact site, leading to the formation of a mature immunological synapse between NK cell and target cell. This may trigger adhesion and secretion of lytic granules and IFN-gamma and activate cytoxicity of activated NK cells. May also promote NK cell-target cell modular exchange, and PVR transfer to the NK cell. This transfer is more important in some tumor cells expressing a lot of PVR, and may trigger fratricide NK cell activation, providing tumors with a mechanism of immunoevasion. Plays a role in mediating tumor cell invasion and migration. {ECO:0000269|PubMed:15471548, ECO:0000269|PubMed:15607800}.; FUNCTION: (Microbial infection) Acts as a receptor for Pseudorabies virus. {ECO:0000269|PubMed:9616127}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Beta3 integrin cell surface interactions;Cell-cell junction organization;Nectin/Necl trans heterodimerization;Adherens junctions interactions;Cell junction organization;Cell-Cell communication;Nectin adhesion pathway (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.311
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.59

Haploinsufficiency Scores

• pHI: 0.0847
• hipred: N
• hipred_score: 0.238
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.706

Gene Damage Prediction

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

Gene ontology

• Biological process: positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target;homophilic cell adhesion via plasma membrane adhesion molecules;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;adherens junction organization;susceptibility to natural killer cell mediated cytotoxicity;positive regulation of natural killer cell mediated cytotoxicity;viral entry into host cell;regulation of immune response;susceptibility to T cell mediated cytotoxicity
• Cellular component: extracellular space;cytoplasm;plasma membrane;cell-cell adherens junction;focal adhesion;cell surface;integral component of membrane
• Molecular function: virus receptor activity;protein binding;signaling receptor activity;protein homodimerization activity;cell adhesion molecule binding