LGALS3

galectin 3, the group of Galectins|Receptor ligands

Basic information

Region (hg38): 14:55124109-55145423

Previous symbols: [ "LGALS2" ]

Links

ENSG00000131981 ∙ NCBI:3958 ∙ OMIM:153619 ∙ HGNC:6563 ∙ Uniprot:P17931 ∙ 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 LGALS3 gene.

• not provided (8 variants)
• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LGALS3 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	2	5
missense			6		1	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	6	3	3

Variants in LGALS3

This is a list of pathogenic ClinVar variants found in the LGALS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-55137391-G-A			Likely benign (Jul 01, 2022)
14-55137398-G-A			Benign (Apr 05, 2018)
14-55138050-T-C			Benign (Jun 12, 2018)
14-55138056-G-A			Likely benign (Dec 01, 2022)
14-55138098-C-T			Likely benign (Dec 01, 2022)
14-55138115-C-G		not specified	Uncertain significance (Sep 07, 2022)
14-55138320-C-T			Benign (Apr 05, 2018)
14-55138346-A-G		not specified	Uncertain significance (Jan 08, 2024)
14-55140318-G-A		not specified	Uncertain significance (Dec 01, 2022)
14-55140354-A-G		not specified	Uncertain significance (Dec 03, 2021)
14-55142637-G-A		not specified	Uncertain significance (Aug 16, 2021)
14-55142650-C-T			Likely benign (Jun 29, 2018)
14-55142697-G-A		not specified	Uncertain significance (Aug 31, 2022)
14-55142700-G-A			Benign (Aug 10, 2018)
14-55145189-G-A		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LGALS3	protein_coding	protein_coding	ENST00000254301	5	21299

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000232	0.516	124741	0	54	124795	0.000216

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.326	130	141	0.923	0.00000734	1582
Missense in Polyphen		35	37.114	0.94305		470
Synonymous	0.582	49	54.5	0.900	0.00000292	530
Loss of Function	0.602	8	10.1	0.795	4.26e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000598	0.000593
Ashkenazi Jewish	0.000199	0.0000993
East Asian	0.000292	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000124
Middle Eastern	0.000292	0.000278
South Asian	0.000361	0.000360
Other	0.000827	0.000825

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Galactose-specific lectin which binds IgE. May mediate with the alpha-3, beta-1 integrin the stimulation by CSPG4 of endothelial cells migration. Together with DMBT1, required for terminal differentiation of columnar epithelial cells during early embryogenesis (By similarity). In the nucleus: acts as a pre-mRNA splicing factor. Involved in acute inflammatory responses including neutrophil activation and adhesion, chemoattraction of monocytes macrophages, opsonization of apoptotic neutrophils, and activation of mast cells. {ECO:0000250, ECO:0000269|PubMed:15181153, ECO:0000269|PubMed:19594635, ECO:0000269|PubMed:19616076}.
• Pathway: AGE-RAGE pathway;Spinal Cord Injury;Transcriptional regulation by RUNX1;Regulation of Ras family activation;RUNX2 regulates genes involved in differentiation of myeloid cells;Transcriptional regulation by RUNX2;Neutrophil degranulation;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Innate Immune System;Immune System;Advanced glycosylation endproduct receptor signaling;RUNX1 regulates transcription of genes involved in differentiation of myeloid cells;Transcriptional regulation by RUNX1;Hedgehog signaling events mediated by Gli proteins (Consensus)

Recessive Scores

• pRec: 0.661

Intolerance Scores

• loftool: 0.839
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.7

Haploinsufficiency Scores

• pHI: 0.341
• hipred: Y
• hipred_score: 0.579
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.490

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lgals3
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; immune system phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); digestive/alimentary phenotype; renal/urinary system phenotype; skeleton phenotype

Gene ontology

• Biological process: monocyte chemotaxis;mRNA processing;RNA splicing;neutrophil chemotaxis;epithelial cell differentiation;regulation of T cell proliferation;neutrophil degranulation;innate immune response;regulation of myeloid cell differentiation;negative regulation of endocytosis;eosinophil chemotaxis;macrophage chemotaxis;negative regulation of T cell receptor signaling pathway;positive chemotaxis;regulation of T cell apoptotic process;mononuclear cell migration;positive regulation of mononuclear cell migration;positive regulation of protein homodimerization activity;positive regulation of calcium ion import;regulation of extrinsic apoptotic signaling pathway via death domain receptors;positive regulation of protein localization to plasma membrane;negative regulation of protein tyrosine phosphatase activity;negative regulation of immunological synapse formation;negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell;positive regulation of dendritic cell differentiation;negative regulation of extrinsic apoptotic signaling pathway
• Cellular component: immunological synapse;extracellular region;extracellular space;nucleus;spliceosomal complex;cytoplasm;mitochondrial inner membrane;plasma membrane;cell surface;membrane;secretory granule membrane;collagen-containing extracellular matrix;extracellular exosome;ficolin-1-rich granule membrane
• Molecular function: RNA binding;protein phosphatase inhibitor activity;protein binding;IgE binding;protein phosphatase binding;carbohydrate binding;chemoattractant activity;laminin binding