ITGA2

integrin subunit alpha 2, the group of Integrin alpha subunits|CD molecules

Basic information

Region (hg38): 5:52989339-53094779

Previous symbols: [ "CD49B" ]

Links

ENSG00000164171 ∙ NCBI:3673 ∙ OMIM:192974 ∙ HGNC:6137 ∙ Uniprot:P17301 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• platelet-type bleeding disorder 9 (Strong), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ITGA2 gene.

• Platelet-type bleeding disorder 9 (202 variants)
• not provided (94 variants)
• Inborn genetic diseases (31 variants)
• Combined molybdoflavoprotein enzyme deficiency (22 variants)
• ITGA2-related condition (4 variants)
• Fetal and neonatal alloimmune thrombocytopenia (1 variants)
• Sulfite oxidase deficiency due to molybdenum cofactor deficiency type B (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGA2 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			3	4	17	24
missense			40	11	17	68
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3	3	6
non coding			75	26	99	200
Total	0	0	120	41	133

Variants in ITGA2

This is a list of pathogenic ClinVar variants found in the ITGA2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-52989345-G-A		Platelet-type bleeding disorder 9	Benign (Jun 20, 2021)
5-52989370-G-C		Platelet-type bleeding disorder 9	Uncertain significance (Jun 14, 2016)
5-52989380-T-A		Platelet-type bleeding disorder 9	Uncertain significance (Jan 13, 2018)
5-52989434-C-T		Platelet-type bleeding disorder 9	Uncertain significance (Jan 13, 2018)
5-52989456-G-A		Platelet-type bleeding disorder 9	Benign (Jan 13, 2018)
5-52989479-A-G		Platelet-type bleeding disorder 9	Benign (Jan 12, 2018)
5-52989482-G-C		Inborn genetic diseases	Uncertain significance (Sep 06, 2022)
5-52989493-G-T		Inborn genetic diseases	Likely benign (Feb 27, 2024)
5-52989814-G-GCA			Benign (Jun 19, 2021)
5-52989814-G-GCACA			Benign (Jun 19, 2021)
5-52989833-CACAG-C			Benign (Jun 19, 2021)
5-52989837-G-C			Benign (Nov 12, 2018)
5-53026539-G-A			Benign (Jun 21, 2021)
5-53026768-G-A			Uncertain significance (Sep 03, 2019)
5-53026806-C-T		Platelet-type bleeding disorder 9	Benign (Jan 12, 2018)
5-53026854-T-A		Platelet-type bleeding disorder 9 • Inborn genetic diseases	Uncertain significance (Dec 26, 2023)
5-53026866-C-A		Inborn genetic diseases	Uncertain significance (Mar 08, 2024)
5-53026878-T-C		Platelet-type bleeding disorder 9 • ITGA2-related disorder	Conflicting classifications of pathogenicity (Apr 25, 2019)
5-53026891-G-T			Benign (Nov 12, 2018)
5-53027152-T-TGATA			Benign (Nov 12, 2018)
5-53041926-A-G			Benign (Nov 12, 2018)
5-53041953-T-C			Benign (Nov 12, 2018)
5-53042078-C-T			Benign (Nov 12, 2018)
5-53042138-G-A		Inborn genetic diseases	Uncertain significance (Jan 04, 2024)
5-53042153-G-A		Platelet-type bleeding disorder 9 • ITGA2-related disorder	Benign/Likely benign (Feb 11, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGA2	protein_coding	protein_coding	ENST00000296585	30	105454

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.28e-11	1.00	125580	0	168	125748	0.000668

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.854	549	608	0.903	0.0000301	7766
Missense in Polyphen		176	220.78	0.79719		2886
Synonymous	-0.768	234	220	1.07	0.0000115	2234
Loss of Function	4.27	29	66.6	0.435	0.00000358	779

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000832	0.000832
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000655	0.000653
Finnish	0.000555	0.000554
European (Non-Finnish)	0.000762	0.000756
Middle Eastern	0.000655	0.000653
South Asian	0.000949	0.000948
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Integrin alpha-2/beta-1 is a receptor for laminin, collagen, collagen C-propeptides, fibronectin and E-cadherin. It recognizes the proline-hydroxylated sequence G-F-P-G-E-R in collagen. It is responsible for adhesion of platelets and other cells to collagens, modulation of collagen and collagenase gene expression, force generation and organization of newly synthesized extracellular matrix.; FUNCTION: (Microbial infection) Integrin ITGA2:ITGB1 acts as a receptor for Human echoviruses 1 and 8. {ECO:0000269|PubMed:8411387}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Platelet activation - 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);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Platelet Aggregation Inhibitor Pathway, Pharmacodynamics;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Integrin-mediated Cell Adhesion;Arrhythmogenic Right Ventricular Cardiomyopathy;Interleukin-11 Signaling Pathway;Human Complement System;Focal Adhesion;TGF-beta 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;Signal Transduction;Integrin cell surface interactions;Laminin interactions;Extracellular matrix organization;Platelet Adhesion to exposed collagen;Integrin;CHL1 interactions;Hemostasis;VEGFR3 signaling in lymphatic endothelium;Arf6 trafficking events;L1CAM interactions;Syndecan interactions;Plexin-D1 Signaling;Non-integrin membrane-ECM interactions;Axon guidance;ECM proteoglycans;MET activates PTK2 signaling;MET promotes cell motility;Signaling by MET;Signaling by Receptor Tyrosine Kinases;Beta1 integrin cell surface interactions;Syndecan-2-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.624

Intolerance Scores

• loftool: 0.501
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.32

Haploinsufficiency Scores

• pHI: 0.278
• hipred: N
• hipred_score: 0.463
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.847

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Itga2
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: response to hypoxia;positive regulation of leukocyte migration;substrate-dependent cell migration;hypotonic response;cell adhesion;cell-matrix adhesion;integrin-mediated signaling pathway;female pregnancy;blood coagulation;cell population proliferation;animal organ morphogenesis;positive regulation of epithelial cell migration;positive regulation of alkaline phosphatase activity;response to amine;response to muscle activity;positive regulation of smooth muscle cell migration;extracellular matrix organization;mammary gland development;positive regulation of cell projection organization;cell-substrate adhesion;positive regulation of collagen biosynthetic process;positive regulation of collagen binding;response to L-ascorbic acid;cell adhesion mediated by integrin;collagen-activated signaling pathway;response to drug;positive regulation of DNA binding;skin morphogenesis;establishment of protein localization;positive regulation of translation;positive regulation of cell adhesion;positive regulation of smooth muscle contraction;viral entry into host cell;focal adhesion assembly;mesodermal cell differentiation;positive regulation of smooth muscle cell proliferation;positive regulation of inflammatory response;positive regulation of positive chemotaxis;detection of mechanical stimulus involved in sensory perception of pain;positive regulation of transmission of nerve impulse;positive regulation of phagocytosis, engulfment;hepatocyte differentiation;response to parathyroid hormone;cellular response to mechanical stimulus;cellular response to estradiol stimulus
• Cellular component: nucleus;plasma membrane;focal adhesion;integrin complex;external side of plasma membrane;cell surface;integrin alpha2-beta1 complex;axon terminus;basal part of cell;perinuclear region of cytoplasm
• Molecular function: amyloid-beta binding;virus receptor activity;integrin binding;protein binding;collagen binding;collagen receptor activity;laminin binding;heparan sulfate proteoglycan binding;protein-containing complex binding;metal ion binding;protein heterodimerization activity;collagen binding involved in cell-matrix adhesion