ITGAL
integrin subunit alpha L, the group of Integrin alpha subunits|CD molecules|MicroRNA protein coding host genes
Basic information
Region (hg38): 16:30472658-30523567
Previous symbols: [ "CD11A" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (80 variants)
- not_provided (7 variants)
- Myoepithelial_tumor (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGAL gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002209.3. 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 | 4 | |||||
| missense | 70 | 10 | 81 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 70 | 11 | 4 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ITGAL | protein_coding | protein_coding | ENST00000356798 | 31 | 50528 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00432 | 0.996 | 125708 | 0 | 40 | 125748 | 0.000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.18 | 521 | 681 | 0.765 | 0.0000386 | 7653 |
| Missense in Polyphen | 87 | 167.85 | 0.51832 | 1835 | ||
| Synonymous | 0.792 | 267 | 284 | 0.940 | 0.0000173 | 2324 |
| Loss of Function | 5.29 | 17 | 62.0 | 0.274 | 0.00000297 | 703 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000428 | 0.000414 |
| Ashkenazi Jewish | 0.000198 | 0.000198 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.000324 | 0.000323 |
| European (Non-Finnish) | 0.000133 | 0.000132 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000980 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Integrin alpha-L/beta-2 is a receptor for ICAM1, ICAM2, ICAM3 and ICAM4. Integrin alpha-L/beta-2 is also a receptor for F11R (PubMed:11812992, PubMed:15528364). Involved in a variety of immune phenomena including leukocyte-endothelial cell interaction, cytotoxic T-cell mediated killing, and antibody dependent killing by granulocytes and monocytes. Contributes to natural killer cell cytotoxicity (PubMed:15356110). Involved in leukocyte adhesion and transmigration of leukocytes including T-cells and neutrophils (PubMed:11812992). Required for generation of common lymphoid progenitor cells in bone marrow, indicating a role in lymphopoiesis (By similarity). Integrin alpha-L/beta-2 in association with ICAM3, contributes to apoptotic neutrophil phagocytosis by macrophages (PubMed:23775590). {ECO:0000250|UniProtKB:P24063, ECO:0000269|PubMed:11812992, ECO:0000269|PubMed:15356110, ECO:0000269|PubMed:15528364, ECO:0000269|PubMed:23775590}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Malaria - Homo sapiens (human);Staphylococcus aureus infection - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Leukocyte transendothelial migration - Homo sapiens (human);Integrin-mediated Cell Adhesion;Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Transcriptional regulation by RUNX3;Neutrophil degranulation;RUNX3 Regulates Immune Response and Cell Migration;Gene expression (Transcription);Transcriptional regulation by RUNX3;Generic Transcription Pathway;Integrin cell surface interactions;RNA Polymerase II Transcription;Extracellular matrix organization;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Integrin;Cell surface interactions at the vascular wall;Hemostasis;Beta2 integrin cell surface interactions
(Consensus)
Recessive Scores
- pRec
- 0.421
Intolerance Scores
- loftool
- 0.374
- rvis_EVS
- -0.86
- rvis_percentile_EVS
- 10.92
Haploinsufficiency Scores
- pHI
- 0.146
- hipred
- N
- hipred_score
- 0.478
- ghis
- 0.567
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.871
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Itgal
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype; neoplasm; immune system phenotype;
Gene ontology
- Biological process
- T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell;phagocytosis;inflammatory response;cell adhesion;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;leukocyte cell-cell adhesion;cell-matrix adhesion;signal transduction;integrin-mediated signaling pathway;extracellular matrix organization;receptor clustering;neutrophil degranulation;regulation of immune response;leukocyte migration;cell-cell adhesion
- Cellular component
- plasma membrane;integrin complex;cell surface;membrane;integrin alphaL-beta2 complex;specific granule membrane;extracellular exosome
- Molecular function
- protein binding;ICAM-3 receptor activity;protein-containing complex binding;metal ion binding;protein heterodimerization activity;cell adhesion molecule binding