LGALS3
galectin 3, the group of Galectins|Receptor ligands
Basic information
Region (hg38): 14:55124110-55145423
Previous symbols: [ "LGALS2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
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 | 5 | |||||
| missense | 8 | |||||
| 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 | 7 | 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) | |||
| 14-55142728-T-G | not specified | Uncertain significance (Jun 16, 2024) | ||
| 14-55145189-G-A | not specified | Uncertain significance (Dec 03, 2021) |
GnomAD
Source:
| 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:
- 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