ITGA5
integrin subunit alpha 5, the group of Integrin alpha subunits|CD molecules
Basic information
Region (hg38): 12:54395261-54419266
Previous symbols: [ "FNRA" ]
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 ITGA5 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 | 5 | |||||
| missense | 46 | 52 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 46 | 2 | 9 |
Variants in ITGA5
This is a list of pathogenic ClinVar variants found in the ITGA5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-54396361-G-A | not specified | Uncertain significance (Mar 14, 2023) | ||
| 12-54397390-C-T | not specified | Uncertain significance (Jul 11, 2023) | ||
| 12-54397391-C-T | not specified | Uncertain significance (Feb 26, 2024) | ||
| 12-54398601-C-T | not specified | Uncertain significance (Nov 30, 2022) | ||
| 12-54398622-C-T | not specified | Likely benign (Mar 31, 2024) | ||
| 12-54398678-G-T | not specified | Uncertain significance (Oct 01, 2024) | ||
| 12-54398698-G-A | not specified | Uncertain significance (Aug 04, 2023) | ||
| 12-54399682-T-C | not specified | Uncertain significance (Jun 01, 2023) | ||
| 12-54399717-G-A | Benign (Jul 26, 2018) | |||
| 12-54399736-A-C | not specified | Uncertain significance (Oct 27, 2022) | ||
| 12-54399751-G-A | not specified | Uncertain significance (Dec 10, 2024) | ||
| 12-54399889-G-A | not specified | Uncertain significance (Apr 28, 2022) | ||
| 12-54399895-C-T | not specified | Uncertain significance (Nov 26, 2024) | ||
| 12-54399910-C-T | not specified | Uncertain significance (Feb 16, 2023) | ||
| 12-54399919-T-C | not specified | Likely benign (Jun 06, 2023) | ||
| 12-54399931-G-A | not specified | Uncertain significance (Dec 16, 2022) | ||
| 12-54399935-C-G | Benign (Sep 10, 2018) | |||
| 12-54400871-T-A | not specified | Uncertain significance (Sep 20, 2023) | ||
| 12-54400895-G-A | not specified | Uncertain significance (Jun 27, 2023) | ||
| 12-54401446-A-C | not specified | Uncertain significance (Jul 30, 2024) | ||
| 12-54401458-A-G | not specified | Uncertain significance (Nov 19, 2024) | ||
| 12-54401483-G-GGAGGAGGGTGGTTTA | Benign (Jul 16, 2018) | |||
| 12-54401600-T-C | not specified | Uncertain significance (Sep 30, 2024) | ||
| 12-54401625-G-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 12-54401626-A-G | Benign (Nov 12, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ITGA5 | protein_coding | protein_coding | ENST00000293379 | 30 | 24200 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.425 | 0.575 | 125723 | 0 | 25 | 125748 | 0.0000994 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.65 | 481 | 594 | 0.809 | 0.0000329 | 6711 |
| Missense in Polyphen | 172 | 255.82 | 0.67235 | 2975 | ||
| Synonymous | 1.08 | 221 | 242 | 0.912 | 0.0000134 | 2167 |
| Loss of Function | 5.88 | 15 | 66.9 | 0.224 | 0.00000356 | 692 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000304 | 0.000304 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000219 | 0.000217 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000709 | 0.0000703 |
| Middle Eastern | 0.000219 | 0.000217 |
| South Asian | 0.000262 | 0.000261 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Integrin alpha-5/beta-1 (ITGA5:ITGB1) is a receptor for fibronectin and fibrinogen. It recognizes the sequence R-G-D in its ligands. ITGA5:ITGB1 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). ITGA5:ITGB1 acts as a receptor for fibrillin-1 (FBN1) and mediates R-G-D-dependent cell adhesion to FBN1 (PubMed:12807887, PubMed:17158881). ITGA5:ITGB1 is a receptor for IL1B and binding is essential for IL1B signaling (PubMed:29030430). {ECO:0000269|PubMed:12807887, ECO:0000269|PubMed:17158881, ECO:0000269|PubMed:18635536, ECO:0000269|PubMed:25398877, ECO:0000269|PubMed:29030430}.; FUNCTION: (Microbial infection) Integrin ITGA2:ITGB1 acts as a receptor for Human parvovirus B19. {ECO:0000269|PubMed:24478423}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Pertussis - Homo sapiens (human);Dilated cardiomyopathy (DCM) - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Phagosome - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Shigellosis - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Integrin-mediated Cell Adhesion;Arrhythmogenic Right Ventricular Cardiomyopathy;Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;EMT transition in Colorectal Cancer;Developmental Biology;RUNX2 regulates genes involved in cell migration;Transcriptional regulation by RUNX2;Gene expression (Transcription);Generic Transcription Pathway;Integrin cell surface interactions;RNA Polymerase II Transcription;Extracellular matrix organization;Elastic fibre formation;Fibronectin matrix formation;Integrin;Cell surface interactions at the vascular wall;Hemostasis;VEGFR3 signaling in lymphatic endothelium;Signal transduction by L1;Arf6 trafficking events;L1CAM interactions;Angiopoietin receptor Tie2-mediated signaling;Plexin-D1 Signaling;Axon guidance;Signaling events mediated by focal adhesion kinase;Beta1 integrin cell surface interactions;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling;Syndecan-4-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.540
Intolerance Scores
- loftool
- rvis_EVS
- -0.86
- rvis_percentile_EVS
- 10.92
Haploinsufficiency Scores
- pHI
- 0.381
- hipred
- Y
- hipred_score
- 0.655
- ghis
- 0.557
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.963
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Itga5
- Phenotype
- embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype; 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); 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); hearing/vestibular/ear 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); immune system phenotype; growth/size/body region phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- itga5
- Affected structure
- interrenal angiogenic sprout
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- angiogenesis;cell-substrate junction assembly;cell adhesion;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;leukocyte cell-cell adhesion;integrin-mediated signaling pathway;female pregnancy;memory;positive regulation of cell-substrate adhesion;extracellular matrix organization;positive regulation of cell migration;positive regulation of vascular endothelial growth factor receptor signaling pathway;cell-substrate adhesion;cell adhesion mediated by integrin;cell-cell adhesion mediated by integrin;heterotypic cell-cell adhesion;wound healing, spreading of epidermal cells;endodermal cell differentiation;viral entry into host cell;positive regulation of peptidyl-tyrosine phosphorylation;leukocyte migration;positive regulation of sprouting angiogenesis;negative regulation of anoikis
- Cellular component
- ruffle;endoplasmic reticulum;Golgi apparatus;plasma membrane;cell-cell junction;focal adhesion;integrin complex;external side of plasma membrane;cell surface;cytoplasmic vesicle;ruffle membrane;synapse;alphav-beta3 integrin-vitronectin complex
- Molecular function
- virus receptor activity;epidermal growth factor receptor binding;platelet-derived growth factor receptor binding;integrin binding;protein binding;vascular endothelial growth factor receptor 2 binding;metal ion binding