LAG3 (Lymphocyte Activating 3) Gene: Structure, Function, and Clinical Significance

A comprehensive biomedical overview of the LAG3 gene, encoding an immune checkpoint receptor, with relevance to cancer immunotherapy and autoimmune diseases.

Gene Information Card

Symbol LAG3
Full Name Lymphocyte Activating 3
Gene Type Protein coding
Chromosomal Location 12p13.32
NCBI Gene ID 3902 ncbi.nlm.nih.gov/gene/3902
Ensembl ID ENSG00000089692
UniProt ID P18627
OMIM ID 153337
HGNC ID 6476
Aliases CD223, LAG-3, FDC, LAG3 protein

Description

The LAG3 gene encodes the lymphocyte activation gene 3 protein, a type I transmembrane protein belonging to the immunoglobulin superfamily. LAG3 is expressed on activated T cells, natural killer (NK) cells, and plasmacytoid dendritic cells, where it negatively regulates T cell activation and proliferation. It binds to MHC class II molecules with high affinity, and its engagement leads to inhibition of T cell receptor signaling. LAG3 is a key immune checkpoint receptor, and its blockade is being explored in cancer immunotherapy. Additionally, LAG3 has been implicated in autoimmune diseases and chronic infections, where its expression on exhausted T cells contributes to immune dysfunction.

Disease Associations

Disease category Pathophysiological mechanism Genomic evidence
Cancer (various types) LAG3 overexpression on tumor-infiltrating lymphocytes leads to T cell exhaustion and immune evasion; blockade enhances anti-tumor immunity. Multiple studies in cancer immunology; clinical trials with anti-LAG3 antibodies (e.g., relatlimab) show efficacy in melanoma.
Autoimmune diseases (e.g., rheumatoid arthritis, type 1 diabetes) LAG3 deficiency or dysfunction may lead to unchecked T cell activation and autoimmunity; LAG3 variants are associated with susceptibility. Genetic association studies and animal models (LAG3 knockout mice develop autoimmune phenotypes).
Chronic viral infections (e.g., HIV, HCV) LAG3 is upregulated on exhausted T cells during chronic infection, contributing to impaired viral control. Observational studies in patient cohorts; functional assays showing LAG3 blockade restores T cell function.
Multiple sclerosis LAG3 may modulate regulatory T cell function; altered expression is observed in peripheral blood. Case-control studies and experimental autoimmune encephalomyelitis (EAE) models.

Expression Profile

Tissue Expression
Tissue nTPM level
Lymph node 0.8 Low
Spleen 0.5 Low
Thymus 0.3 Low
Bone marrow 0.2 Low
Blood 0.1 Low
Cell Line Expression
Cell Line nTPM Notes
Jurkat (T cell leukemia) 0.1 Low baseline; inducible upon activation
K562 (chronic myelogenous leukemia) 0.0 Not expressed
A549 (lung carcinoma) 0.0 Not expressed
MCF7 (breast carcinoma) 0.0 Not expressed
HEK293 (embryonic kidney) 0.0 Not expressed
Data source:Human Protein Atlas(proteinatlas.org)

Mutations & Variants

Hotspot Mutations
Variant Type Frequency Functional Description
rs870849 (C/T) SNP (intronic) Allele frequency: C=0.35, T=0.65 (global) Associated with altered LAG3 expression and autoimmune disease risk in some studies.
rs1882543 (A/G) SNP (intronic) Allele frequency: A=0.30, G=0.70 Potential impact on splicing; linked to multiple sclerosis susceptibility.
c.539C>T (p.Pro180Leu) Missense Rare (MAF <0.01) Located in extracellular domain; may affect MHC class II binding.
c.847G>A (p.Val283Met) Missense Rare (MAF <0.01) In transmembrane domain; potential effect on signaling.
Mutation functional classification

Loss of Function (LOF)

Loss-of-function mutations in LAG3 are rare but have been reported in autoimmune conditions, leading to reduced inhibitory signaling and enhanced T cell activation.

Gain of Function (GOF)

Gain-of-function mutations that increase LAG3 expression or signaling are not well characterized; however, overexpression in tumors is common and contributes to immune evasion.

Dominant Negative (DN)

No dominant-negative mutations have been described for LAG3.

Pathways

• T cell receptor signaling pathway (KEGG hsa04660)
• PD-1/PD-L1 checkpoint pathway (KEGG hsa05235)
• Immune checkpoint regulation (Reactome: R-HSA-389948)
• Costimulation by the CD28 family (Reactome: R-HSA-388841)

Protein Summary

The LAG3 protein (CD223) is a 498-amino acid type I transmembrane glycoprotein with four extracellular immunoglobulin-like domains (D1-D4). The D1 domain contains a unique 'extra loop' that is critical for MHC class II binding. LAG3 is expressed on activated T cells, NK cells, and plasmacytoid dendritic cells. It negatively regulates T cell activation by competing with CD4 for MHC class II binding and by transmitting inhibitory signals via its cytoplasmic domain. LAG3 is cleaved by ADAM10/17 metalloproteases, releasing a soluble form (sLAG3) that can be detected in serum. LAG3 plays a role in regulatory T cell function and is a target for cancer immunotherapy.

Related Products

Product name Cat.No. Species Gene ID
LAG3 Knockout HEK293 Cell Line EDJ-KQ17690 Human 3902 Details Get a Quote
LAG3 Knockout HeLa Cell Line EDJ-KQ19777 Human 3902 Details Get a Quote
LAG3 Knockout A-549 Cell Line EDJ-KQ62251 Human 3902 Details Get a Quote
LAG3 Knockout HCT 116 Cell Line EDJ-KQ70736 Human 3902 Details Get a Quote
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