ITGB1
integrin subunit beta 1, the group of Integrin beta subunits|CD molecules
Basic information
Region (hg38): 10:32887272-33005792
Previous symbols: [ "FNRB", "MSK12", "MDF2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (20 variants)
- not provided (6 variants)
- Neural tube defect (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGB1 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 | |||||
| missense | 18 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 2 | 2 | ||||
| non coding ? | 2 | |||||
| Total | 0 | 0 | 19 | 3 | 2 |
Variants in ITGB1
This is a list of pathogenic ClinVar variants found in the ITGB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-32907089-C-T | not specified | Uncertain significance (Apr 04, 2023) | ||
| 10-32908395-C-CT | Neural tube defect | risk factor (Jan 01, 2013) | ||
| 10-32908447-C-T | Esophageal atresia;Pyloric stenosis | Uncertain significance (May 22, 2019) | ||
| 10-32908460-A-C | not specified | Uncertain significance (Jan 26, 2023) | ||
| 10-32908514-T-A | not specified | Uncertain significance (Jun 22, 2023) | ||
| 10-32908529-G-C | not specified | Uncertain significance (Oct 13, 2023) | ||
| 10-32910213-G-A | Likely benign (Dec 28, 2018) | |||
| 10-32910360-C-A | not specified | Uncertain significance (Apr 07, 2022) | ||
| 10-32911497-G-C | not specified | Uncertain significance (Aug 15, 2023) | ||
| 10-32911570-G-A | Benign (Dec 31, 2019) | |||
| 10-32911628-T-C | not specified | Uncertain significance (Mar 01, 2023) | ||
| 10-32911891-C-T | not specified | Uncertain significance (Jul 09, 2021) | ||
| 10-32911903-T-C | not specified | Uncertain significance (Feb 27, 2023) | ||
| 10-32912050-T-A | not specified | Uncertain significance (Oct 25, 2023) | ||
| 10-32912060-T-G | not specified | Uncertain significance (Oct 12, 2022) | ||
| 10-32912110-C-T | not specified | Uncertain significance (Dec 15, 2023) | ||
| 10-32919993-A-G | not specified | Uncertain significance (Jan 12, 2024) | ||
| 10-32920297-T-G | not specified | Uncertain significance (Aug 08, 2023) | ||
| 10-32920331-T-C | not specified | Uncertain significance (May 11, 2022) | ||
| 10-32920355-C-T | not specified | Likely benign (Dec 06, 2022) | ||
| 10-32922291-C-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 10-32922666-T-G | not specified | Uncertain significance (Mar 29, 2022) | ||
| 10-32922694-T-G | not specified | Uncertain significance (Jun 03, 2022) | ||
| 10-32922708-G-C | not specified | Uncertain significance (Oct 12, 2021) | ||
| 10-32923577-G-A | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ITGB1 | protein_coding | protein_coding | ENST00000396033 | 15 | 105474 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.982 | 0.0179 | 125713 | 0 | 12 | 125725 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.46 | 227 | 429 | 0.530 | 0.0000218 | 5328 |
| Missense in Polyphen | 53 | 189.7 | 0.27939 | 2384 | ||
| Synonymous | 0.501 | 142 | 150 | 0.948 | 0.00000829 | 1395 |
| Loss of Function | 4.87 | 6 | 38.7 | 0.155 | 0.00000181 | 524 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000306 | 0.000305 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000356 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Integrins alpha-1/beta-1, alpha-2/beta-1, alpha-10/beta- 1 and alpha-11/beta-1 are receptors for collagen. Integrins alpha- 1/beta-1 and alpha-2/beta-2 recognize the proline-hydroxylated sequence G-F-P-G-E-R in collagen. Integrins alpha-2/beta-1, alpha- 3/beta-1, alpha-4/beta-1, alpha-5/beta-1, alpha-8/beta-1, alpha- 10/beta-1, alpha-11/beta-1 and alpha-V/beta-1 are receptors for fibronectin. Alpha-4/beta-1 recognizes one or more domains within the alternatively spliced CS-1 and CS-5 regions of fibronectin. Integrin alpha-5/beta-1 is a receptor for fibrinogen. Integrin alpha-1/beta-1, alpha-2/beta-1, alpha-6/beta-1 and alpha-7/beta-1 are receptors for lamimin. Integrin alpha-4/beta-1 is a receptor for VCAM1. It recognizes the sequence Q-I-D-S in VCAM1. Integrin alpha-9/beta-1 is a receptor for VCAM1, cytotactin and osteopontin. It recognizes the sequence A-E-I-D-G-I-E-L in cytotactin. Integrin alpha-3/beta-1 is a receptor for epiligrin, thrombospondin and CSPG4. Alpha-3/beta-1 may mediate with LGALS3 the stimulation by CSPG4 of endothelial cells migration. Integrin alpha-V/beta-1 is a receptor for vitronectin. Beta-1 integrins recognize the sequence R-G-D in a wide array of ligands. Isoform 2 interferes with isoform 1 resulting in a dominant negative effect on cell adhesion and migration (in vitro). When associated with alpha-7/beta-1 integrin, regulates cell adhesion and laminin matrix deposition. Involved in promoting endothelial cell motility and angiogenesis. Involved in osteoblast compaction through the fibronectin fibrillogenesis cell-mediated matrix assembly process and the formation of mineralized bone nodules. May be involved in up-regulation of the activity of kinases such as PKC via binding to KRT1. Together with KRT1 and RACK1, serves as a platform for SRC activation or inactivation. Plays a mechanistic adhesive role during telophase, required for the successful completion of cytokinesis. Integrin alpha-3/beta-1 provides a docking site for FAP (seprase) at invadopodia plasma membranes in a collagen- dependent manner and hence may participate in the adhesion, formation of invadopodia and matrix degradation processes, promoting cell invasion. ITGA4:ITGB1 binds to fractalkine (CX3CL1) and may act as its coreceptor in CX3CR1-dependent fractalkine signaling (PubMed:23125415, PubMed:24789099). ITGA4:ITGB1 and ITGA5:ITGB1 bind to PLA2G2A via a site (site 2) which is distinct from the classical ligand-binding site (site 1) and this induces integrin conformational changes and enhanced ligand binding to site 1 (PubMed:18635536, PubMed:25398877). ITGA5:ITGB1 acts as a receptor for fibrillin-1 (FBN1) and mediates R-G-D-dependent cell adhesion to FBN1 (PubMed:12807887, PubMed:17158881). ITGA5:ITGB1 is a receptor for IL1B and binding is essential for IL1B signaling (PubMed:29030430). {ECO:0000269|PubMed:10455171, ECO:0000269|PubMed:12473654, ECO:0000269|PubMed:12807887, ECO:0000269|PubMed:16256741, ECO:0000269|PubMed:17158881, ECO:0000269|PubMed:18635536, ECO:0000269|PubMed:18804435, ECO:0000269|PubMed:19064666, ECO:0000269|PubMed:21768292, ECO:0000269|PubMed:23125415, ECO:0000269|PubMed:24789099, ECO:0000269|PubMed:25398877, ECO:0000269|PubMed:29030430, ECO:0000269|PubMed:7523423}.; FUNCTION: (Microbial infection) Integrin ITGA2:ITGB1 acts as a receptor for Human echoviruses 1 and 8. {ECO:0000269|PubMed:8411387}.; FUNCTION: (Microbial infection) Acts as a receptor for Epstein- Barr virus/HHV-4. {ECO:0000269|PubMed:17945327}.; FUNCTION: (Microbial infection) Integrin ITGA2:ITGB1 acts as a receptor for Human rotavirus. {ECO:0000269|PubMed:12941907}.; FUNCTION: (Microbial infection) In case of HIV-1 infection, integrin ITGA5:ITGB1 binding to extracellular viral Tat protein seems to enhance angiogenesis in Kaposi's sarcoma lesions. {ECO:0000269|PubMed:10397733}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Platelet activation - Homo sapiens (human);Cell adhesion molecules (CAMs) - Homo sapiens (human);ECM-receptor interaction - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Pertussis - Homo sapiens (human);Dilated cardiomyopathy (DCM) - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Tight junction - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Phagosome - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Axon guidance - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Shigellosis - Homo sapiens (human);Pathogenic Escherichia coli infection - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Integrin-mediated Cell Adhesion;Prolactin Signaling Pathway;Neural Crest Differentiation;Arrhythmogenic Right Ventricular Cardiomyopathy;Pathogenic Escherichia coli infection;Primary Focal Segmental Glomerulosclerosis FSGS;JAK-STAT;Focal Adhesion;Signaling of Hepatocyte Growth Factor Receptor;Rac1-Pak1-p38-MMP-2 pathway;RHO GTPases Activate Formins;TGF-beta Signaling Pathway;Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling;VEGFA-VEGFR2 Signaling Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Interleukin-4 and 13 signaling;PI3K-Akt Signaling Pathway;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Developmental Biology;Signal Transduction;erk and pi-3 kinase are necessary for collagen binding in corneal epithelia;ucalpain and friends in cell spread;integrin signaling pathway;MET interacts with TNS proteins;pten dependent cell cycle arrest and apoptosis;b cell survival pathway;mcalpain and friends in cell motility;Prolactin;Integrin cell surface interactions;Laminin interactions;Extracellular matrix organization;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Molecules associated with elastic fibres;Elastic fibre formation;Fibronectin matrix formation;RHO GTPases Activate Formins;Platelet Adhesion to exposed collagen;RHO GTPase Effectors;Signaling by Rho GTPases;Integrin;CHL1 interactions;EGFR1;agrin in postsynaptic differentiation;Cell surface interactions at the vascular wall;Hemostasis;Signaling events mediated by TCPTP;Other semaphorin interactions;Semaphorin interactions;VEGFR3 signaling in lymphatic endothelium;a6b1 and a6b4 Integrin signaling;Signal transduction by L1;Gastrin;Arf6 trafficking events;L1CAM interactions;Angiopoietin receptor Tie2-mediated signaling;Syndecan interactions;Plexin-D1 Signaling;Non-integrin membrane-ECM interactions;Axon guidance;ECM proteoglycans;Basigin interactions;Localization of the PINCH-ILK-PARVIN complex to focal adhesions;MET activates PTK2 signaling;Cell-extracellular matrix interactions;MET promotes cell motility;Signaling by MET;Cell junction organization;Signaling by Receptor Tyrosine Kinases;Cell-Cell communication;a4b7 Integrin signaling;Alpha9 beta1 integrin signaling events;Validated targets of C-MYC transcriptional repression;Signaling events mediated by focal adhesion kinase;Beta1 integrin cell surface interactions;Reelin signaling pathway;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling;Alpha4 beta1 integrin signaling events;Syndecan-4-mediated signaling events;Syndecan-2-mediated signaling events;RhoA signaling pathway;Signaling events mediated by PRL
(Consensus)
Recessive Scores
- pRec
- 0.852
Intolerance Scores
- loftool
- 0.0195
- rvis_EVS
- -1.18
- rvis_percentile_EVS
- 5.94
Haploinsufficiency Scores
- pHI
- 0.936
- hipred
- Y
- hipred_score
- 0.613
- ghis
- 0.685
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.826
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Itgb1
- Phenotype
- craniofacial phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland 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); hematopoietic system phenotype; growth/size/body region phenotype; reproductive system phenotype; normal 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); 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); vision/eye phenotype; digestive/alimentary phenotype; limbs/digits/tail 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); hearing/vestibular/ear phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; pigmentation phenotype; neoplasm;
Zebrafish Information Network
- Gene name
- itgb1a
- Affected structure
- dorsal longitudinal anastomotic vessel
- Phenotype tag
- abnormal
- Phenotype quality
- decreased occurrence
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;in utero embryonic development;cell fate specification;cell migration involved in sprouting angiogenesis;phagocytosis;cellular defense response;homophilic cell adhesion via plasma membrane adhesion molecules;leukocyte cell-cell adhesion;cell-matrix adhesion;calcium-independent cell-matrix adhesion;transforming growth factor beta receptor signaling pathway;integrin-mediated signaling pathway;positive regulation of cell population proliferation;germ cell migration;visual learning;regulation of collagen catabolic process;cell migration;cytokine-mediated signaling pathway;formation of radial glial scaffolds;cell projection organization;lamellipodium assembly;B cell differentiation;extracellular matrix organization;cell-substrate adhesion;receptor internalization;cell adhesion mediated by integrin;cell-cell adhesion mediated by integrin;heterotypic cell-cell adhesion;negative regulation of Rho protein signal transduction;positive regulation of apoptotic process;stress fiber assembly;positive regulation of GTPase activity;sarcomere organization;negative regulation of cell differentiation;positive regulation of angiogenesis;viral entry into host cell;mesodermal cell differentiation;axon extension;dendrite morphogenesis;regulation of immune response;modulation of chemical synaptic transmission;leukocyte migration;leukocyte tethering or rolling;regulation of cell cycle;positive regulation of protein kinase B signaling;cardiac muscle cell differentiation;cellular response to low-density lipoprotein particle stimulus;basement membrane organization;positive regulation of protein localization to plasma membrane;positive regulation of signaling receptor activity;negative regulation of anoikis
- Cellular component
- ruffle;cytoplasm;plasma membrane;focal adhesion;integrin complex;external side of plasma membrane;cell surface;intercalated disc;membrane;lamellipodium;filopodium;neuromuscular junction;cleavage furrow;ruffle membrane;integrin alpha1-beta1 complex;integrin alpha2-beta1 complex;integrin alpha3-beta1 complex;integrin alpha7-beta1 complex;integrin alpha8-beta1 complex;integrin alpha10-beta1 complex;integrin alpha11-beta1 complex;myelin sheath abaxonal region;sarcolemma;melanosome;dendritic spine;receptor complex;membrane raft;perinuclear region of cytoplasm;recycling endosome;extracellular exosome;invadopodium membrane;glial cell projection;Schaffer collateral - CA1 synapse;glutamatergic synapse;integral component of synaptic membrane
- Molecular function
- virus receptor activity;fibronectin binding;protease binding;actin binding;integrin binding;protein binding;coreceptor activity;C-X3-C chemokine binding;laminin binding;protein-containing complex binding;cadherin binding;metal ion binding;protein heterodimerization activity;cell adhesion molecule binding;collagen binding involved in cell-matrix adhesion