ITGA1
integrin subunit alpha 1, the group of Integrin alpha subunits|CD molecules
Basic information
Region (hg38): 5:52787916-52959209
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (183 variants)
- not_provided (11 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 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. These statistics are base on transcript: NM_000181501.2. 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 | |||||
| missense | 138 | 143 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 138 | 5 | 6 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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