ITGAV
integrin subunit alpha V, the group of Integrin alpha subunits|CD molecules
Basic information
Region (hg38): 2:186590010-186680901
Previous symbols: [ "VNRA", "MSK8", "VTNR" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- ITGAV deficiency (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGAV 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 | |||||
| missense | 87 | 90 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 2 | 1 | 87 | 2 | 4 |
Variants in ITGAV
This is a list of pathogenic ClinVar variants found in the ITGAV region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-186590355-G-A | not specified | Uncertain significance (Nov 26, 2024) | ||
| 2-186590367-G-T | not specified | Uncertain significance (Apr 24, 2024) | ||
| 2-186590396-C-T | not specified | Uncertain significance (Dec 07, 2021) | ||
| 2-186590405-C-T | not specified | Uncertain significance (Feb 21, 2024) | ||
| 2-186590411-C-G | not specified | Uncertain significance (Oct 08, 2024) | ||
| 2-186590415-C-T | not specified | Uncertain significance (Nov 22, 2021) | ||
| 2-186590440-C-G | not specified | Uncertain significance (Oct 26, 2022) | ||
| 2-186590506-C-G | not specified | Uncertain significance (Aug 12, 2021) | ||
| 2-186602022-C-T | not specified | Uncertain significance (Sep 18, 2024) | ||
| 2-186602025-A-G | not specified | Uncertain significance (Aug 11, 2022) | ||
| 2-186602059-C-T | Uncertain significance (Feb 01, 2024) | |||
| 2-186602067-C-G | not specified | Uncertain significance (Sep 26, 2022) | ||
| 2-186602121-C-T | not specified | Uncertain significance (Jul 17, 2024) | ||
| 2-186602122-G-A | not specified | Uncertain significance (Feb 28, 2023) | ||
| 2-186602133-A-G | not specified | Uncertain significance (Jul 14, 2023) | ||
| 2-186602143-A-G | not specified | Uncertain significance (Apr 25, 2022) | ||
| 2-186625496-G-C | ITGAV deficiency | Pathogenic (Nov 22, 2023) | ||
| 2-186625505-G-A | Benign (Aug 18, 2018) | |||
| 2-186625519-G-A | not specified | Uncertain significance (Oct 04, 2022) | ||
| 2-186625534-C-A | not specified | Uncertain significance (Feb 07, 2023) | ||
| 2-186636116-A-G | ITGAV-related disorder | Likely benign (Jun 12, 2024) | ||
| 2-186636125-C-T | Benign (Dec 27, 2017) | |||
| 2-186636128-C-A | not specified | Uncertain significance (Jan 23, 2024) | ||
| 2-186636147-A-G | not specified | Uncertain significance (Dec 20, 2023) | ||
| 2-186636171-C-T | not specified | Uncertain significance (Sep 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ITGAV | protein_coding | protein_coding | ENST00000261023 | 30 | 90837 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000228 | 1.00 | 125712 | 0 | 36 | 125748 | 0.000143 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.888 | 505 | 564 | 0.895 | 0.0000289 | 6825 |
| Missense in Polyphen | 173 | 224.12 | 0.77191 | 2769 | ||
| Synonymous | 0.441 | 195 | 203 | 0.961 | 0.0000105 | 2009 |
| Loss of Function | 5.13 | 19 | 62.9 | 0.302 | 0.00000325 | 749 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000281 | 0.000269 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000161 | 0.000158 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.000489 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: The alpha-V (ITGAV) integrins are receptors for vitronectin, cytotactin, fibronectin, fibrinogen, laminin, matrix metalloproteinase-2, osteopontin, osteomodulin, prothrombin, thrombospondin and vWF. They recognize the sequence R-G-D in a wide array of ligands. ITGAV:ITGB3 binds to fractalkine (CX3CL1) and may act as its coreceptor in CX3CR1-dependent fractalkine signaling (PubMed:23125415). ITGAV:ITGB3 binds to NRG1 (via EGF domain) and this binding is essential for NRG1-ERBB signaling (PubMed:20682778). ITGAV:ITGB3 binds to FGF1 and this binding is essential for FGF1 signaling (PubMed:18441324). ITGAV:ITGB3 binds to FGF2 and this binding is essential for FGF2 signaling (PubMed:28302677). ITGAV:ITGB3 binds to IGF1 and this binding is essential for IGF1 signaling (PubMed:19578119). ITGAV:ITGB3 binds to IGF2 and this binding is essential for IGF2 signaling (PubMed:28873464). ITGAV:ITGB3 binds to IL1B and this binding is essential for IL1B signaling (PubMed:29030430). ITGAV:ITGB3 binds to PLA2G2A via a site (site 2) which is distinct from the classical ligand-binding site (site 1) and this induces integrin conformational changes and enhanced ligand binding to site 1 (PubMed:18635536, PubMed:25398877). ITGAV:ITGB3 and ITGAV:ITGB6 act as a receptor for fibrillin-1 (FBN1) and mediate R-G-D- dependent cell adhesion to FBN1 (PubMed:12807887, PubMed:17158881). Integrin alpha-V/beta-6 or alpha-V/beta-8 (ITGAV:ITGB6 or ITGAV:ITGB8) mediates R-G-D-dependent release of transforming growth factor beta-1 (TGF-beta-1) from regulatory Latency-associated peptide (LAP), thereby playing a key role in TGF-beta-1 activation (PubMed:15184403, PubMed:22278742, PubMed:28117447). {ECO:0000269|PubMed:12807887, ECO:0000269|PubMed:15184403, ECO:0000269|PubMed:17158881, ECO:0000269|PubMed:18441324, ECO:0000269|PubMed:18635536, ECO:0000269|PubMed:19578119, ECO:0000269|PubMed:20682778, ECO:0000269|PubMed:22278742, ECO:0000269|PubMed:23125415, ECO:0000269|PubMed:25398877, ECO:0000269|PubMed:28117447, ECO:0000269|PubMed:28302677, ECO:0000269|PubMed:28873464, ECO:0000269|PubMed:29030430}.; FUNCTION: (Microbial infection) Integrin ITGAV:ITGB5 and ITGAV:ITGB3 act as receptors for Coxsackievirus A9 and B1. {ECO:0000269|PubMed:15194773, ECO:0000269|PubMed:7519807, ECO:0000269|PubMed:9426447}.; FUNCTION: (Microbial infection) Integrin ITGAV:ITGB6 acts as a receptor for herpes simplex 1/HHV-1. {ECO:0000269|PubMed:24367260}.; FUNCTION: (Microbial infection) Integrin ITGAV:ITGB3 acts as a receptor for West nile virus. {ECO:0000269|PubMed:23658209}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Cell adhesion molecules (CAMs) - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Dilated cardiomyopathy (DCM) - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Phagosome - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);VEGF Signaling Pathway;Osteopontin Signaling;Integrin-mediated Cell Adhesion;Arrhythmogenic Right Ventricular Cardiomyopathy;Primary Focal Segmental Glomerulosclerosis FSGS;Focal Adhesion;Osteoblast Signaling;MFAP5-mediated ovarian cancer cell motility and invasiveness;VEGFA-VEGFR2 Signaling Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Developmental Biology;Neutrophil degranulation;Signal Transduction;phospholipids as signalling intermediaries;VEGFA-VEGFR2 Pathway;Integrin cell surface interactions;Laminin interactions;Extracellular matrix organization;Innate Immune System;Immune System;Adaptive Immune System;Molecules associated with elastic fibres;Elastic fibre formation;Fibroblast growth factor-1;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Beta3 integrin cell surface interactions;Integrin;PECAM1 interactions;Cell surface interactions at the vascular wall;Hemostasis;Signal transduction by L1;Cross-presentation of particulate exogenous antigens (phagosomes);Signaling by VEGF;Arf6 trafficking events;L1CAM interactions;Syndecan interactions;Plexin-D1 Signaling;Non-integrin membrane-ECM interactions;Axon guidance;ECM proteoglycans;Signaling by Receptor Tyrosine Kinases;Osteopontin-mediated events;Nectin adhesion pathway;Beta5 beta6 beta7 and beta8 integrin cell surface interactions;Signaling events mediated by focal adhesion kinase;Beta1 integrin cell surface interactions;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling;PDGFR-beta signaling pathway;Signaling events mediated by VEGFR1 and VEGFR2;PDGFR-alpha signaling pathway;Integrins in angiogenesis
(Consensus)
Recessive Scores
- pRec
- 0.598
Intolerance Scores
- loftool
- 0.178
- rvis_EVS
- -1.48
- rvis_percentile_EVS
- 3.69
Haploinsufficiency Scores
- pHI
- 0.708
- hipred
- Y
- hipred_score
- 0.747
- ghis
- 0.600
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.844
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Itgav
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; craniofacial phenotype; muscle phenotype; cellular phenotype; immune system phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); 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; renal/urinary system phenotype;
Zebrafish Information Network
- Gene name
- itgav
- Affected structure
- caudal vein plexus
- Phenotype tag
- abnormal
- Phenotype quality
- decreased diameter
Gene ontology
- Biological process
- angiogenesis;vasculogenesis;antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;cell adhesion;cell-matrix adhesion;positive regulation of cytosolic calcium ion concentration;integrin-mediated signaling pathway;positive regulation of cell population proliferation;negative regulation of macrophage derived foam cell differentiation;negative regulation of lipid storage;extracellular matrix organization;positive regulation of cell migration;cell-substrate adhesion;negative regulation of lipid transport;cell adhesion mediated by integrin;positive regulation of osteoblast proliferation;heterotypic cell-cell adhesion;substrate adhesion-dependent cell spreading;endodermal cell differentiation;apolipoprotein A-I-mediated signaling pathway;transforming growth factor-beta secretion;apoptotic cell clearance;neutrophil degranulation;negative regulation of low-density lipoprotein particle receptor biosynthetic process;positive regulation of cell adhesion;viral entry into host cell;vascular endothelial growth factor receptor signaling pathway;negative regulation of lipoprotein metabolic process;regulation of phagocytosis;leukocyte migration;negative chemotaxis;entry of symbiont into host cell by promotion of host phagocytosis;ERK1 and ERK2 cascade;calcium ion transmembrane transport;extrinsic apoptotic signaling pathway in absence of ligand;regulation of transforming growth factor beta activation;negative regulation of entry of bacterium into host cell;negative regulation of extrinsic apoptotic signaling pathway
- Cellular component
- cytosol;plasma membrane;integral component of plasma membrane;focal adhesion;integrin complex;external side of plasma membrane;cell surface;membrane;lamellipodium membrane;filopodium membrane;microvillus membrane;ruffle membrane;integrin alphav-beta3 complex;integrin alphav-beta5 complex;integrin alphav-beta6 complex;integrin alphav-beta8 complex;specific granule membrane;alphav-beta3 integrin-PKCalpha complex;alphav-beta3 integrin-IGF-1-IGF1R complex;alphav-beta3 integrin-HMGB1 complex;phagocytic vesicle;extracellular exosome
- Molecular function
- virus receptor activity;opsonin binding;fibronectin binding;protease binding;protein kinase C binding;integrin binding;voltage-gated calcium channel activity;protein binding;coreceptor activity;fibroblast growth factor binding;C-X3-C chemokine binding;insulin-like growth factor I binding;neuregulin binding;metal ion binding;transforming growth factor beta binding;extracellular matrix binding;extracellular matrix protein binding