ITGA1

integrin subunit alpha 1, the group of Integrin alpha subunits|CD molecules

Basic information

Region (hg38): 5:52787915-52959209

Links

ENSG00000213949 ∙ NCBI:3672 ∙ OMIM:192968 ∙ HGNC:6134 ∙ Uniprot:P56199 ∙ 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 ITGA1 gene.

• Inborn genetic diseases (50 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGA1 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				1	3	4
missense			36		2	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding			14			14
Total	0	0	50	1	5

Variants in ITGA1

This is a list of pathogenic ClinVar variants found in the ITGA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-52788369-C-A		not specified	Uncertain significance (Aug 28, 2023)
5-52788402-T-C		not specified	Uncertain significance (Jul 20, 2022)
5-52800432-C-T		not specified	Uncertain significance (Mar 01, 2023)
5-52800570-A-G		not specified	Uncertain significance (Dec 01, 2022)
5-52800576-T-C		not specified	Uncertain significance (Apr 27, 2023)
5-52800812-G-C		not specified	Uncertain significance (Aug 17, 2022)
5-52800902-A-C		not specified	Uncertain significance (Aug 08, 2022)
5-52800915-A-C		not specified	Uncertain significance (Dec 15, 2023)
5-52800969-C-A		not specified	Uncertain significance (Feb 15, 2023)
5-52800971-A-G		not specified	Uncertain significance (Jun 21, 2022)
5-52801476-G-T		not specified	Uncertain significance (Jan 23, 2023)
5-52801510-A-T		not specified	Uncertain significance (Sep 06, 2022)
5-52801525-C-G		not specified	Uncertain significance (Jan 31, 2024)
5-52801532-A-G		not specified	Uncertain significance (Aug 30, 2022)
5-52801594-A-C		not specified	Uncertain significance (Apr 12, 2023)
5-52801668-A-G		not specified	Uncertain significance (Jan 11, 2023)
5-52801679-G-C		not specified	Uncertain significance (Jun 17, 2022)
5-52801709-G-C		not specified	Uncertain significance (Nov 21, 2023)
5-52801763-G-A		not specified	Uncertain significance (Jul 26, 2022)
5-52801835-G-C		not specified	Uncertain significance (May 15, 2023)
5-52849373-C-T		not specified	Uncertain significance (Nov 21, 2022)
5-52861503-A-G		not specified	Uncertain significance (Nov 10, 2022)
5-52861506-A-G		not specified	Uncertain significance (Feb 21, 2024)
5-52861513-A-G			Benign (Jul 31, 2018)
5-52865029-G-C		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGA1	protein_coding	protein_coding	ENST00000282588	29	171311

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.61e-16	1.00	125673	0	74	125747	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.981	548	617	0.889	0.0000307	7707
Missense in Polyphen		160	214.64	0.74543		2696
Synonymous	-0.625	236	224	1.05	0.0000120	2244
Loss of Function	3.27	36	64.3	0.559	0.00000345	798

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000482	0.000482
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000326	0.000326
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000338	0.000334
Middle Eastern	0.000326	0.000326
South Asian	0.000393	0.000392
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Integrin alpha-1/beta-1 is a receptor for laminin and collagen. It recognizes the proline-hydroxylated sequence G-F-P-G- E-R in collagen. Involved in anchorage-dependent, negative regulation of EGF-stimulated cell growth. {ECO:0000269|PubMed:15592458}.
• Pathway: PI3K-Akt signaling pathway - 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);Regulation of actin cytoskeleton - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Integrin-mediated Cell Adhesion;Arrhythmogenic Right Ventricular Cardiomyopathy;miRNA targets in ECM and membrane receptors;Focal Adhesion;Signaling of Hepatocyte Growth Factor Receptor;NOTCH1 regulation of human endothelial cell calcification;PI3K-Akt Signaling Pathway;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Regulation of Actin Cytoskeleton;Developmental Biology;Smooth Muscle Contraction;erk and pi-3 kinase are necessary for collagen binding in corneal epithelia;ucalpain and friends in cell spread;integrin signaling pathway;b cell survival pathway;mcalpain and friends in cell motility;Integrin cell surface interactions;Laminin interactions;Extracellular matrix organization;Platelet Adhesion to exposed collagen;Muscle contraction;Integrin;CHL1 interactions;agrin in postsynaptic differentiation;Hemostasis;Signaling events mediated by TCPTP;Other semaphorin interactions;Semaphorin interactions;VEGFR3 signaling in lymphatic endothelium;Arf6 trafficking events;L1CAM interactions;Plexin-D1 Signaling;Axon guidance;Beta1 integrin cell surface interactions;Signaling events mediated by PRL (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.416
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.89

Haploinsufficiency Scores

• pHI: 0.524
• hipred: Y
• hipred_score: 0.589
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.458

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itga1
• Phenotype: renal/urinary system phenotype; immune 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); 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); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: activation of MAPK activity;muscle contraction;cell-matrix adhesion;integrin-mediated signaling pathway;negative regulation of cell population proliferation;extracellular matrix organization;neutrophil chemotaxis;positive regulation of phosphoprotein phosphatase activity;negative regulation of epidermal growth factor receptor signaling pathway;vasodilation;positive regulation of neuron apoptotic process;cellular extravasation;neuron projection morphogenesis
• Cellular component: acrosomal vesicle;plasma membrane;focal adhesion;integrin complex;external side of plasma membrane;cell surface;membrane;integrin alpha1-beta1 complex;neuron projection;perikaryon;membrane raft;basal part of cell;extracellular exosome
• Molecular function: signaling receptor binding;protein binding;collagen binding;protein phosphatase binding;metal ion binding;collagen binding involved in cell-matrix adhesion