PVR
Basic information
Region (hg38): 19:44643798-44666162
Previous symbols: [ "PVS" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | |||||
| missense | 53 | 61 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 53 | 10 | 4 |
GnomAD
Source:
| 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:
- 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