ITGA7

integrin subunit alpha 7, the group of Integrin alpha subunits

Basic information

Region (hg38): 12:55684568-55716404

Links

ENSG00000135424

∙ NCBI:3679 ∙ OMIM:600536 ∙ HGNC:6143 ∙ Uniprot:Q13683 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

congenital fiber-type disproportion myopathy (Supportive), mode of inheritance: AD
congenital muscular dystrophy due to integrin alpha-7 deficiency (Supportive), mode of inheritance: AR
congenital muscular dystrophy due to integrin alpha-7 deficiency (Strong), mode of inheritance: AR
congenital muscular dystrophy due to integrin alpha-7 deficiency (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, congenital, due to integrin alpha-7 deficiency	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic	9590299; 19260934

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ITGA7 gene.

Congenital_muscular_dystrophy_due_to_integrin_alpha-7_deficiency (886 variants)
not_specified (212 variants)
not_provided (183 variants)
ITGA7-related_disorder (28 variants)
Congenital_Muscular_Dystrophy,_ITGA7-related (1 variants)
Abnormal_brain_morphology (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGA7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002206.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	225 clinvar	6 clinvar	237
missense		1 clinvar	440 clinvar	22 clinvar	4 clinvar	467
nonsense	8 clinvar	14 clinvar	1 clinvar			23
start loss			1			1
frameshift	15 clinvar	11 clinvar	1 clinvar			27
splice donor/acceptor (+/-2bp)	2 clinvar	12 clinvar				14
Total	25	38	449	247	10

Highest pathogenic variant AF is 0.000095412164

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITGA7	protein_coding	protein_coding	ENST00000553804	25	31476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.27e-17	0.994	125534	0	214	125748	0.000851

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.359	637	663	0.961	0.0000415	7337
Missense in Polyphen		206	224.83	0.91625		2491
Synonymous	0.273	275	281	0.979	0.0000173	2383
Loss of Function	2.83	36	59.5	0.605	0.00000349	618

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00123	0.00123
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00120	0.00120
Finnish	0.000421	0.000416
European (Non-Finnish)	0.00106	0.00105
Middle Eastern	0.00120	0.00120
South Asian	0.000785	0.000784
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

Function: FUNCTION: Integrin alpha-7/beta-1 is the primary laminin receptor on skeletal myoblasts and adult myofibers. During myogenic differentiation, it may induce changes in the shape and mobility of myoblasts, and facilitate their localization at laminin-rich sites of secondary fiber formation. It is involved in the maintenance of the myofibers cytoarchitecture as well as for their anchorage, viability and functional integrity. Isoform Alpha-7X2B and isoform Alpha-7X1B promote myoblast migration on laminin 1 and laminin 2/4, but isoform Alpha-7X1B is less active on laminin 1 (In vitro). Acts as Schwann cell receptor for laminin-2. Acts as a receptor of COMP and mediates its effect on vascular smooth muscle cells (VSMCs) maturation (By similarity). Required to promote contractile phenotype acquisition in differentiated airway smooth muscle (ASM) cells. {ECO:0000250, ECO:0000269|PubMed:10694445, ECO:0000269|PubMed:17641293, ECO:0000269|PubMed:9307969}.;
Disease: DISEASE: Muscular dystrophy congenital due to integrin alpha-7 deficiency (MDCI) [MIM:613204]: A form of congenital muscular dystrophy. Patients present at birth, or within the first few months of life, with hypotonia, muscle weakness and often with joint contractures. {ECO:0000269|PubMed:9590299}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
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);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;Integrin cell surface interactions;Laminin interactions;Extracellular matrix organization;Integrin;Arf6 trafficking events;Plexin-D1 Signaling;ECM proteoglycans;Beta1 integrin cell surface interactions (Consensus)

Recessive Scores

pRec: 0.366

Intolerance Scores

loftool: 0.935
rvis_EVS: 0.17
rvis_percentile_EVS: 65.35

Haploinsufficiency Scores

pHI: 0.268
hipred: Y
hipred_score: 0.635
ghis: 0.479

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.751

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Itga7
Phenotype: growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton 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);

Zebrafish Information Network

Gene name: itga7
Affected structure: skeletal muscle cell
Phenotype tag: abnormal
Phenotype quality: retracted

Gene ontology

Biological process: cell-matrix adhesion;integrin-mediated signaling pathway;muscle organ development;regulation of cell shape;extracellular matrix organization;heterotypic cell-cell adhesion;endodermal cell differentiation
Cellular component: plasma membrane;integrin complex;cell surface
Molecular function: protein binding;metal ion binding