VAV2
vav guanine nucleotide exchange factor 2, the group of Dbl family Rho GEFs|SH2 domain containing|Pleckstrin homology domain containing
Basic information
Region (hg38): 9:133761893-133992604
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAV2 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 | 8 | |||||
| missense | 46 | 46 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | 3 | 5 | ||
| non coding | 3 | |||||
| Total | 0 | 0 | 46 | 5 | 6 |
Variants in VAV2
This is a list of pathogenic ClinVar variants found in the VAV2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-133764086-G-A | Likely benign (Jun 15, 2018) | |||
| 9-133768433-G-T | Benign (Apr 04, 2018) | |||
| 9-133768444-G-A | not specified | Uncertain significance (Dec 16, 2023) | ||
| 9-133768483-C-T | not specified | Uncertain significance (May 17, 2023) | ||
| 9-133768518-C-T | not specified | Uncertain significance (Aug 13, 2021) | ||
| 9-133768523-C-T | not specified | Likely benign (Mar 29, 2024) | ||
| 9-133769432-C-T | not specified | Uncertain significance (May 13, 2022) | ||
| 9-133770407-G-A | not specified | Uncertain significance (Feb 28, 2023) | ||
| 9-133772008-T-C | not specified | Uncertain significance (May 13, 2024) | ||
| 9-133772041-T-C | not specified | Uncertain significance (Dec 03, 2021) | ||
| 9-133772055-A-ACACACGGCCCCGGCGGTCACTGCGTGAGGGC | Benign (Dec 31, 2019) | |||
| 9-133774963-C-T | not specified | Uncertain significance (Dec 05, 2022) | ||
| 9-133774966-C-A | not specified | Uncertain significance (Apr 26, 2023) | ||
| 9-133775000-G-A | Benign (Jul 05, 2018) | |||
| 9-133776040-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
| 9-133776055-C-T | not specified | Uncertain significance (Aug 23, 2021) | ||
| 9-133776056-G-A | not specified | Uncertain significance (Jan 08, 2024) | ||
| 9-133777449-T-G | not specified | Uncertain significance (May 21, 2024) | ||
| 9-133777459-C-T | not specified | Uncertain significance (Nov 09, 2023) | ||
| 9-133777468-C-G | Benign (May 24, 2018) | |||
| 9-133778813-C-G | Benign (Dec 31, 2019) | |||
| 9-133779936-C-T | not specified | Uncertain significance (Nov 09, 2021) | ||
| 9-133779937-G-A | Benign (Jul 26, 2018) | |||
| 9-133779939-C-T | not specified | Uncertain significance (Mar 18, 2024) | ||
| 9-133783518-G-T | not specified | Uncertain significance (May 09, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VAV2 | protein_coding | protein_coding | ENST00000371850 | 30 | 230711 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000311 | 1.00 | 125718 | 0 | 30 | 125748 | 0.000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.49 | 436 | 533 | 0.819 | 0.0000324 | 5817 |
| Missense in Polyphen | 125 | 193.22 | 0.64692 | 2145 | ||
| Synonymous | -0.868 | 237 | 221 | 1.07 | 0.0000151 | 1567 |
| Loss of Function | 4.44 | 20 | 55.8 | 0.358 | 0.00000255 | 655 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000350 | 0.000333 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000165 | 0.000163 |
| Finnish | 0.0000475 | 0.0000462 |
| European (Non-Finnish) | 0.000116 | 0.000114 |
| Middle Eastern | 0.000165 | 0.000163 |
| South Asian | 0.000164 | 0.000163 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Guanine nucleotide exchange factor for the Rho family of Ras-related GTPases. Plays an important role in angiogenesis. Its recruitment by phosphorylated EPHA2 is critical for EFNA1-induced RAC1 GTPase activation and vascular endothelial cell migration and assembly (By similarity). {ECO:0000250}.;
- Pathway
- Focal adhesion - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);B cell receptor signaling pathway - Homo sapiens (human);Fc epsilon RI signaling pathway - Homo sapiens (human);Fc gamma R-mediated phagocytosis - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Integrin-mediated Cell Adhesion;Prolactin Signaling Pathway;B Cell Receptor Signaling Pathway;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;JAK-STAT;Focal Adhesion;Hepatitis C and Hepatocellular Carcinoma;VEGFA-VEGFR2 Signaling Pathway;Chemokine signaling pathway;Microglia Pathogen Phagocytosis Pathway;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;EGF-EGFR Signaling Pathway;Developmental Biology;Signaling by GPCR;Signal Transduction;DAP12 signaling;DAP12 interactions;VEGFA-VEGFR2 Pathway;phosphoinositides and their downstream targets;Prolactin;Fcgamma receptor (FCGR) dependent phagocytosis;EPH-Ephrin signaling;FCERI mediated MAPK activation;FCERI mediated Ca+2 mobilization;Fc epsilon receptor (FCERI) signaling;TCR;Innate Immune System;Immune System;EPH-ephrin mediated repulsion of cells;Rho GTPase cycle;BCR;GPVI-mediated activation cascade;Platelet activation, signaling and aggregation;Signaling by Rho GTPases;BDNF;EGFR1;Regulation of RAC1 activity;ErbB1 downstream signaling;Hemostasis;NRAGE signals death through JNK;BCR signaling pathway;Regulation of actin dynamics for phagocytic cup formation;Death Receptor Signalling;p75 NTR receptor-mediated signalling;Signal transduction by L1;Signaling by VEGF;L1CAM interactions;EPO signaling pathway;Axon guidance;G alpha (12/13) signalling events;Signaling by Receptor Tyrosine Kinases;GPCR downstream signalling;Regulation of CDC42 activity;Nectin adhesion pathway;CDC42 signaling events;Cell death signalling via NRAGE, NRIF and NADE;PDGFR-beta signaling pathway;EPHA2 forward signaling;E-cadherin signaling in the nascent adherens junction;EPHA forward signaling;Regulation of RhoA activity;VEGFR2 mediated vascular permeability
(Consensus)
Recessive Scores
- pRec
- 0.301
Intolerance Scores
- loftool
- 0.198
- rvis_EVS
- -1.7
- rvis_percentile_EVS
- 2.55
Haploinsufficiency Scores
- pHI
- 0.721
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.647
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.953
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vav2
- Phenotype
- immune system phenotype; renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; vision/eye phenotype; hematopoietic 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); cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- angiogenesis;signal transduction;G protein-coupled receptor signaling pathway;small GTPase mediated signal transduction;regulation of cell size;cell migration;lamellipodium assembly;platelet activation;regulation of Rho protein signal transduction;Fc-epsilon receptor signaling pathway;Fc-gamma receptor signaling pathway involved in phagocytosis;positive regulation of apoptotic process;regulation of GTPase activity;positive regulation of phosphatidylinositol 3-kinase activity;vascular endothelial growth factor receptor signaling pathway;ephrin receptor signaling pathway;regulation of small GTPase mediated signal transduction
- Cellular component
- cytosol;plasma membrane
- Molecular function
- phosphotyrosine residue binding;guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;epidermal growth factor receptor binding;protein binding;metal ion binding