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

ENSG00000005844 ∙ NCBI:3683 ∙ OMIM:153370 ∙ HGNC:6148 ∙ Uniprot:P20701 ∙ 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 ITGAL gene.

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.

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					3	3
missense			25	4	2	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	25	4	6

Variants in ITGAL

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

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

Position	Type	Phenotype	Significance	ClinVar
16-30474199-C-T		not specified	Uncertain significance (Aug 12, 2021)
16-30474235-G-A		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
16-30479194-G-A			Benign (May 14, 2018)
16-30481518-C-T		not specified	Likely benign (Sep 04, 2024)
16-30481575-A-G		not specified	Uncertain significance (Oct 01, 2024)
16-30483841-G-A		not specified	Uncertain significance (Dec 02, 2024)
16-30484178-G-A			Benign (Aug 20, 2018)
16-30484180-G-A		not specified	Uncertain significance (Aug 27, 2024)
16-30484214-G-C		not specified	Uncertain significance (Oct 17, 2023)
16-30484222-A-T		not specified	Uncertain significance (Mar 11, 2024)
16-30489160-G-A			Benign (Mar 29, 2018)
16-30489260-G-A		not specified	Uncertain significance (Sep 06, 2022)
16-30489395-T-G			Benign (Jul 31, 2018)
16-30494220-G-C		not specified	Uncertain significance (Jun 11, 2021)
16-30494239-G-A		not specified	Likely benign (Oct 27, 2022)
16-30494280-C-G		not specified	Uncertain significance (Nov 08, 2024)
16-30494293-G-A		not specified	Likely benign (Oct 17, 2024)
16-30494746-G-A		not specified	Likely benign (Aug 01, 2022)
16-30494771-C-T		not specified	Uncertain significance (Apr 23, 2024)
16-30494792-C-A		not specified	Uncertain significance (Aug 04, 2024)
16-30494833-A-G		not specified	Likely benign (Apr 15, 2024)
16-30496151-C-T		not specified	Uncertain significance (Jun 13, 2024)
16-30496152-G-A		not specified	Uncertain significance (Aug 17, 2022)
16-30496172-G-T		not specified	Uncertain significance (Nov 04, 2022)
16-30496235-C-G		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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