ITGAE
protein-codingintegrin subunit alpha E, the group of CD molecules|Integrin alpha subunits
Gene summary
Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This gene encodes an I-domain-containing alpha integrin that undergoes post-translational cleavage in the extracellular domain, yielding disulfide-linked heavy and light chains. In combination with the beta 7 integrin, this protein forms the E-cadherin binding integrin known as the human mucosal lymphocyte-1 antigen. This protein is preferentially expressed in human intestinal intraepithelial lymphocytes (IEL), and in addition to a role in adhesion, it may serve as an accessory molecule for IEL activation. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~86.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ITGAE variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002208.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 5 | 8 | |||
| missense | 188 | 20 | 208 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 194 | 25 | 0 | 219 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002199.3 | 31 | MANE Select | |
| Ensembl | ENSP00000263087.4 | 31 | MANE Select | |
| RefSeq | NP_001412000.1 | 30 | Standard | |
| RefSeq | NP_001412001.1 | 29 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Regulation of actin cytoskeleton - Homo sapiens (human)
- Integrin-mediated Cell Adhesion
- Focal Adhesion
- Focal Adhesion-PI3K-Akt-mTOR-signaling pathway
- Integrin cell surface interactions
Biological Process
- cell adhesion
- integrin-mediated signaling pathway
- extracellular matrix organization
Molecular Function
- metal ion binding
Cellular Component
- plasma membrane
- integrin complex
- external side of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000263087
- Coding exons
- 31
- Length
- 86616
- Individuals with no LoFs
- 125562
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 186
- Defined
- 125748
- p
- 0.000740
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.236 | 676 | 693 | 0.975 | 0.0000399 | 7695 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00092 | 0.00092 | rare |
| Latino/Admixed American | 0.00069 | 0.00069 | rare |
| Ashkenazi Jewish | 0.00041 | 0.00040 | rare |
| East Asian | 0.00039 | 0.00038 | rare |
| Finnish | 0.0012 | 0.0012 | notable |
| European (Non-Finnish) | 0.00076 | 0.00076 | rare |
| South Asian | 0.00074 | 0.00072 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
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.;
Intolerance Scores
- LoFtool
- 0.490
- RVIS EVS
- 0.77
- RVIS percentile EVS
- 86.91
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.616
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |