ITGB6
integrin subunit beta 6, the group of Integrin beta subunits
Basic information
Region (hg38): 2:160099667-160271888
Links
Phenotypes
GenCC
Source:
- amelogenesis imperfecta type 1 (Supportive), mode of inheritance: AD
- amelogenesis imperfecta, type 3A (Supportive), mode of inheritance: AD
- amelogenesis imperfecta type 1H (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Amelogenesis imperfecta, type IH | 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 | Dental | 24305999; 24319098 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (106 variants)
- not_provided (39 variants)
- Amelogenesis_imperfecta_type_1H (12 variants)
- ITGB6-related_disorder (11 variants)
- Prostate_cancer (1 variants)
- Adolescent_alopeciam_dentogingival_abnormalitites_and_intellectual_disability (1 variants)
- not_specified (1 variants)
- Microcephaly (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGB6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000888.5. 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 | 17 | 26 | ||||
| missense | 110 | 125 | ||||
| nonsense | 3 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 5 | 3 | 111 | 24 | 12 |
Highest pathogenic variant AF is 0.0000369412
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ITGB6 | protein_coding | protein_coding | ENST00000283249 | 15 | 172223 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.63e-22 | 0.00264 | 125643 | 0 | 105 | 125748 | 0.000418 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.694 | 478 | 437 | 1.09 | 0.0000235 | 5192 |
| Missense in Polyphen | 197 | 186.43 | 1.0567 | 2202 | ||
| Synonymous | -0.189 | 172 | 169 | 1.02 | 0.0000104 | 1489 |
| Loss of Function | 0.394 | 35 | 37.6 | 0.931 | 0.00000188 | 466 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000680 | 0.000680 |
| Ashkenazi Jewish | 0.000596 | 0.000595 |
| East Asian | 0.000545 | 0.000544 |
| Finnish | 0.0000470 | 0.0000462 |
| European (Non-Finnish) | 0.000539 | 0.000528 |
| Middle Eastern | 0.000545 | 0.000544 |
| South Asian | 0.000268 | 0.000261 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Integrin alpha-V:beta-6 (ITGAV:ITGB6) is a receptor for fibronectin and cytotactin (PubMed:17545607, PubMed:17158881). It recognizes the sequence R-G-D in its ligands (PubMed:17545607, PubMed:17158881). Internalisation of integrin alpha-V/beta-6 via clathrin-mediated endocytosis promotes carcinoma cell invasion (PubMed:17545607, PubMed:17158881). ITGAV:ITGB6 acts as a receptor for fibrillin-1 (FBN1) and mediates R-G-D-dependent cell adhesion to FBN1 (PubMed:17158881). Integrin alpha-V:beta-6 (ITGAV:ITGB6) mediates R-G-D-dependent release of transforming growth factor beta-1 (TGF-beta-1) from regulatory Latency-associated peptide (LAP), thereby playing a key role in TGF-beta-1 activation (PubMed:15184403, PubMed:22278742, PubMed:28117447). {ECO:0000269|PubMed:15184403, ECO:0000269|PubMed:17158881, ECO:0000269|PubMed:17545607, ECO:0000269|PubMed:22278742, ECO:0000269|PubMed:28117447}.; FUNCTION: (Microbial infection) Integrin ITGAV:ITGB6 acts as a receptor for Herpes simplex virus-1/HHV-1 (PubMed:24367260). {ECO:0000269|PubMed:24367260}.;
- Disease
- DISEASE: Amelogenesis imperfecta 1H (AI1H) [MIM:616221]: A disorder characterized by defective enamel formation, resulting in hypoplastic and hypomineralized tooth enamel that may be rough, pitted, and/or discolored. {ECO:0000269|PubMed:24305999, ECO:0000269|PubMed:24319098}. 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;miRNA targets in ECM and membrane receptors;Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;TGF-beta Receptor Signaling;Integrin cell surface interactions;Extracellular matrix organization;Molecules associated with elastic fibres;Elastic fibre formation;Integrin;ECM proteoglycans;Beta5 beta6 beta7 and beta8 integrin cell surface interactions
(Consensus)
Recessive Scores
- pRec
- 0.259
Intolerance Scores
- loftool
- 0.223
- rvis_EVS
- -0.59
- rvis_percentile_EVS
- 18.23
Haploinsufficiency Scores
- pHI
- 0.498
- hipred
- Y
- hipred_score
- 0.602
- ghis
- 0.432
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.666
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Itgb6
- Phenotype
- homeostasis/metabolism 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); immune system phenotype; hematopoietic system phenotype; respiratory system phenotype;
Gene ontology
- Biological process
- inflammatory response;cell adhesion;cell-matrix adhesion;integrin-mediated signaling pathway;cell migration;extracellular matrix organization;cell adhesion mediated by integrin;transforming growth factor-beta secretion;viral entry into host cell;regulation of transforming growth factor beta activation
- Cellular component
- nucleoplasm;centrosome;plasma membrane;focal adhesion;integrin complex;external side of plasma membrane;cell surface;cell junction;integrin alphav-beta6 complex;receptor complex
- Molecular function
- virus receptor activity;integrin binding;protein binding;signaling receptor activity