ITGAE

integrin subunit alpha E, the group of CD molecules|Integrin alpha subunits

Basic information

Region (hg38): 17:3714628-3801188

Links

ENSG00000083457NCBI:3682OMIM:604682HGNC:6147Uniprot:P38570AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ITGAE gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
5
missense
163
clinvar
20
clinvar
183
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 163 25 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ITGAEprotein_codingprotein_codingENST00000263087 3186616
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.92e-200.84012556201861257480.000740
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2366766930.9750.00003997695
Missense in Polyphen190218.160.870942684
Synonymous0.7992692860.9400.00001782317
Loss of Function2.284058.90.6790.00000267702

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001620.00162
Ashkenazi Jewish0.0004150.000397
East Asian0.0003850.000381
Finnish0.001200.00120
European (Non-Finnish)0.0007620.000756
Middle Eastern0.0003850.000381
South Asian0.0007360.000719
Other0.0003260.000326

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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