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

ENSG00000073008NCBI:5817OMIM:173850HGNC:9705Uniprot:P15151AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • not_specified (58 variants)
  • PVR-related_disorder (9 variants)
  • not_provided (1 variants)

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. These statistics are base on transcript: NM_000006505.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
2
clinvar
6
missense
53
clinvar
6
clinvar
2
clinvar
61
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 53 10 4
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PVRprotein_codingprotein_codingENST00000425690 819753
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.92e-100.1871257140331257470.000131
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9992092540.8230.00001592641
Missense in Polyphen5473.8710.731810
Synonymous1.90871130.7720.00000768890
Loss of Function0.5731618.70.8579.77e-7196

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002110.000210
Ashkenazi Jewish0.000.00
East Asian0.0005460.000544
Finnish0.000.00
European (Non-Finnish)0.0001090.000105
Middle Eastern0.0005460.000544
South Asian0.0001960.000196
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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