ITGA5

integrin subunit alpha 5, the group of Integrin alpha subunits|CD molecules

Basic information

Region (hg38): 12:54395260-54419266

Previous symbols: [ "FNRA" ]

Links

ENSG00000161638 ∙ NCBI:3678 ∙ OMIM:135620 ∙ HGNC:6141 ∙ Uniprot:P08648 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ITGA5 gene.

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	5
missense			46	2	4	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)
12-54398698-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 (Jun 30, 2022)
12-54399889-G-A		not specified	Uncertain significance (Apr 28, 2022)
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)
12-54401458-A-G		not specified	Uncertain significance (Oct 06, 2022)
12-54401483-G-GGAGGAGGGTGGTTTA			Benign (Jul 16, 2018)
12-54401625-G-A		not specified	Uncertain significance (Sep 16, 2021)
12-54401626-A-G			Benign (Nov 12, 2018)
12-54401822-G-T		not specified	Uncertain significance (Jan 03, 2024)
12-54402060-C-T		not specified	Uncertain significance (Jul 12, 2023)
12-54402061-G-A			Benign (Dec 31, 2019)
12-54402202-G-A		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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