ITGA7
Basic information
Region (hg38): 12:55684568-55716404
Links
Phenotypes
GenCC
Source:
- congenital merosin-deficient muscular dystrophy 1A (Definitive), mode of inheritance: AR
- 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
Clinical Genomic Database
Source:
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
- Congenital muscular dystrophy due to integrin alpha-7 deficiency (21 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.
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 | 193 | 207 | ||||
missense | 402 | 10 | 417 | |||
nonsense | 11 | 21 | ||||
start loss | 1 | |||||
frameshift | 12 | 22 | ||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 9 | |||||
splice region | 24 | 43 | 5 | 72 | ||
non coding | 124 | 44 | 177 | |||
Total | 21 | 28 | 422 | 327 | 58 |
Highest pathogenic variant AF is 0.0000131
Variants in ITGA7
This is a list of pathogenic ClinVar variants found in the ITGA7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
12-55684886-GA-G | Congenital Muscular Dystrophy, ITGA7-related | Uncertain significance (Jun 14, 2016) | ||
12-55685063-C-T | Congenital muscular dystrophy due to integrin alpha-7 deficiency • not specified | Uncertain significance (Sep 26, 2023) | ||
12-55685067-G-A | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Likely benign (Jul 03, 2023) | ||
12-55685067-G-C | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Likely benign (Jan 23, 2020) | ||
12-55685076-T-C | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Likely benign (Jul 16, 2023) | ||
12-55685078-G-C | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Uncertain significance (Apr 06, 2022) | ||
12-55685084-C-T | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Uncertain significance (Aug 23, 2022) | ||
12-55685085-A-G | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Likely benign (Aug 09, 2022) | ||
12-55685087-C-T | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Uncertain significance (Sep 22, 2022) | ||
12-55685088-G-A | not specified • Congenital muscular dystrophy due to integrin alpha-7 deficiency | Benign/Likely benign (Feb 01, 2024) | ||
12-55685099-C-G | Congenital muscular dystrophy due to integrin alpha-7 deficiency • not specified | Uncertain significance (Oct 18, 2022) | ||
12-55685099-C-T | Congenital muscular dystrophy due to integrin alpha-7 deficiency • not specified | Uncertain significance (Aug 10, 2023) | ||
12-55685100-G-A | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Likely benign (Nov 22, 2023) | ||
12-55685108-C-T | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Uncertain significance (Aug 10, 2022) | ||
12-55685109-G-A | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Likely benign (Dec 06, 2023) | ||
12-55685117-C-T | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Uncertain significance (Jan 28, 2022) | ||
12-55685119-A-G | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Uncertain significance (Feb 14, 2020) | ||
12-55685123-T-C | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Uncertain significance (Jul 17, 2022) | ||
12-55685123-T-G | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Uncertain significance (May 26, 2021) | ||
12-55685124-G-A | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Likely benign (Oct 13, 2022) | ||
12-55685124-G-C | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Likely benign (Jun 04, 2022) | ||
12-55685130-T-G | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Likely benign (Nov 28, 2023) | ||
12-55685136-C-T | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Likely benign (Jun 01, 2023) | ||
12-55685137-G-A | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Uncertain significance (Aug 31, 2022) | ||
12-55685137-G-C | Congenital muscular dystrophy due to integrin alpha-7 deficiency | Uncertain significance (Sep 07, 2022) |
GnomAD
Source:
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:
- 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