LAG3

lymphocyte activating 3, the group of CD molecules|Immunoglobulin like domain containing

Basic information

Region (hg38): 12:6772511-6778455

Links

ENSG00000089692 ∙ NCBI:3902 ∙ OMIM:153337 ∙ HGNC:6476 ∙ Uniprot:P18627 ∙ 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 LAG3 gene.

• Inborn genetic diseases (35 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAG3 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				1		1
missense			31	4	2	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	31	5	2

Variants in LAG3

This is a list of pathogenic ClinVar variants found in the LAG3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-6772917-C-T			Benign (Aug 21, 2018)
12-6773222-C-G		not specified	Uncertain significance (Mar 01, 2023)
12-6773266-A-G		not specified	Uncertain significance (Feb 05, 2024)
12-6773714-C-A		not specified	Uncertain significance (Aug 16, 2022)
12-6773717-C-A		not specified	Uncertain significance (Oct 25, 2022)
12-6773725-C-T		not specified	Uncertain significance (Jun 22, 2021)
12-6773732-C-T		not specified	Uncertain significance (Dec 17, 2023)
12-6773857-G-T		not specified	Uncertain significance (May 01, 2022)
12-6773866-G-A		not specified	Uncertain significance (Oct 18, 2021)
12-6773911-C-T		not specified	Uncertain significance (Mar 08, 2024)
12-6773966-C-G		not specified	Uncertain significance (Sep 27, 2021)
12-6773993-A-G		not specified	Uncertain significance (Mar 22, 2023)
12-6774604-G-A		not specified	Uncertain significance (Nov 09, 2021)
12-6774646-A-G		not specified	Uncertain significance (Aug 17, 2022)
12-6774670-G-A		not specified	Uncertain significance (Aug 17, 2022)
12-6774684-C-T		not specified	Uncertain significance (Feb 16, 2023)
12-6774694-G-A		not specified	Uncertain significance (Aug 02, 2023)
12-6774699-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-6774711-C-G		not specified	Uncertain significance (Dec 01, 2022)
12-6774730-C-G		not specified	Uncertain significance (May 18, 2023)
12-6774733-C-T		not specified	Uncertain significance (Jul 09, 2021)
12-6774743-C-G		not specified	Uncertain significance (Aug 03, 2022)
12-6774747-G-T		not specified	Uncertain significance (Sep 01, 2021)
12-6774858-G-A		not specified	Uncertain significance (Sep 27, 2021)
12-6775278-G-A		not specified	Uncertain significance (Jan 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAG3	protein_coding	protein_coding	ENST00000203629	8	5944

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.276	0.724	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.512	246	270	0.912	0.0000150	3277
Missense in Polyphen		51	66.113	0.7714		808
Synonymous	-0.887	127	115	1.11	0.00000638	1173
Loss of Function	3.24	5	21.0	0.238	0.00000114	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in lymphocyte activation. Binds to HLA class-II antigens.
• Pathway: MHC class II antigen presentation;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.399
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.54

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.273
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.299

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lag3
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: cell surface receptor signaling pathway;antigen processing and presentation of exogenous peptide antigen via MHC class II;negative regulation of interleukin-2 biosynthetic process;positive regulation of natural killer cell mediated cytotoxicity;negative regulation of T cell activation
• Cellular component: plasma membrane;external side of plasma membrane;integral component of membrane
• Molecular function: antigen binding;transmembrane signaling receptor activity;MHC class II protein binding