ITGAE

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

Basic information

Region (hg38): 17:3714627-3801188

Links

ENSG00000083457 ∙ NCBI:3682 ∙ OMIM:604682 ∙ HGNC:6147 ∙ Uniprot:P38570 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (66 variants)
• not provided (7 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5		5
missense			42	6	1	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			16	2		18
Total	0	0	58	13	1

Variants in ITGAE

This is a list of pathogenic ClinVar variants found in the ITGAE region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-3720332-A-T		not specified	Uncertain significance (Aug 03, 2022)
17-3723307-G-A		not specified	Uncertain significance (Jan 12, 2024)
17-3723355-C-T		not specified	Uncertain significance (Apr 04, 2023)
17-3723726-A-G		not specified	Uncertain significance (Aug 17, 2021)
17-3723957-C-T		not specified	Uncertain significance (Jun 23, 2023)
17-3723991-C-T		not specified	Uncertain significance (Aug 19, 2023)
17-3724062-T-G		not specified	Uncertain significance (Dec 01, 2022)
17-3724081-G-A		not specified	Uncertain significance (Sep 21, 2023)
17-3724114-C-A		not specified	Uncertain significance (Nov 06, 2023)
17-3724136-C-A		not specified	Uncertain significance (Jan 30, 2024)
17-3724168-G-A		not specified	Likely benign (Aug 13, 2021)
17-3724218-A-G		not specified	Uncertain significance (Aug 02, 2022)
17-3724232-G-T		not specified	Uncertain significance (Dec 12, 2023)
17-3724234-G-C		not specified	Uncertain significance (Feb 27, 2023)
17-3724251-C-T		not specified	Uncertain significance (Mar 29, 2023)
17-3724306-A-G		not specified	Uncertain significance (Mar 06, 2023)
17-3724336-G-C		not specified	Uncertain significance (Aug 02, 2023)
17-3724356-C-G		not specified	Uncertain significance (Nov 09, 2023)
17-3724363-C-T		not specified	Uncertain significance (Jun 18, 2021)
17-3724380-G-C		not specified	Uncertain significance (Jul 13, 2021)
17-3724419-C-G		not specified	Likely benign (Jun 21, 2023)
17-3724442-C-G		not specified	Uncertain significance (Mar 07, 2024)
17-3724447-C-G		not specified	Uncertain significance (Dec 15, 2023)
17-3724474-C-G		not specified	Uncertain significance (Jun 21, 2023)
17-3724510-C-T		not specified	Uncertain significance (Dec 19, 2023)

GnomAD

Source: gnomAD

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: 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

	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