ITGAE
Basic information
Region (hg38): 17:3714628-3801188
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (307 variants)
- not_provided (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITGAE gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002208.5. 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 | 5 | |||||
missense | 163 | 20 | 183 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 163 | 25 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ITGAE | protein_coding | protein_coding | ENST00000263087 | 31 | 86616 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.92e-20 | 0.840 | 125562 | 0 | 186 | 125748 | 0.000740 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.236 | 676 | 693 | 0.975 | 0.0000399 | 7695 |
Missense in Polyphen | 190 | 218.16 | 0.87094 | 2684 | ||
Synonymous | 0.799 | 269 | 286 | 0.940 | 0.0000178 | 2317 |
Loss of Function | 2.28 | 40 | 58.9 | 0.679 | 0.00000267 | 702 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00162 | 0.00162 |
Ashkenazi Jewish | 0.000415 | 0.000397 |
East Asian | 0.000385 | 0.000381 |
Finnish | 0.00120 | 0.00120 |
European (Non-Finnish) | 0.000762 | 0.000756 |
Middle Eastern | 0.000385 | 0.000381 |
South Asian | 0.000736 | 0.000719 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Integrin alpha-E/beta-7 is a receptor for E-cadherin. It mediates adhesion of intra-epithelial T-lymphocytes to epithelial cell monolayers.;
- Pathway
- Regulation of actin cytoskeleton - Homo sapiens (human);Integrin-mediated Cell Adhesion;Focal Adhesion;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Integrin cell surface interactions;Extracellular matrix organization;Integrin;AlphaE beta7 integrin cell surface interactions;E-cadherin signaling in the nascent adherens junction
(Consensus)
Intolerance Scores
- loftool
- 0.490
- rvis_EVS
- 0.77
- rvis_percentile_EVS
- 86.91
Haploinsufficiency Scores
- pHI
- 0.110
- hipred
- N
- hipred_score
- 0.233
- ghis
- 0.432
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.616
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Itgae
- Phenotype
- immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- cell adhesion;integrin-mediated signaling pathway;extracellular matrix organization
- Cellular component
- plasma membrane;integrin complex;external side of plasma membrane
- Molecular function
- metal ion binding