LGALS3
protein-codinggalectin 3, the group of Galectins|Receptor ligands
Gene summary
This gene encodes a member of the galectin family of carbohydrate binding proteins. Members of this protein family have an affinity for beta-galactosides. The encoded protein is characterized by an N-terminal proline-rich tandem repeat domain and a single C-terminal carbohydrate recognition domain. This protein can self-associate through the N-terminal domain allowing it to bind to multivalent saccharide ligands. This protein localizes to the extracellular matrix, the cytoplasm and the nucleus. This protein plays a role in numerous cellular functions including apoptosis, innate immunity, cell adhesion and T-cell regulation. The protein exhibits antimicrobial activity against bacteria and fungi. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Oct 2014]
- LGALS2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LGALS3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002306.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 4 | 2 | 9 | ||
| missense | 36 | 1 | 37 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 46 | 4 | 3 | 53 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002297.2 | 5 | MANE Select | |
| Ensembl | ENSP00000254301.9 | 5 | MANE Select | |
| RefSeq | NP_001344607.1 | 6 | Standard | |
| Ensembl | ENSP00000451526.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- AGE-RAGE pathway
- Spinal Cord Injury
- Transcriptional regulation by RUNX1
- Regulation of Ras family activation
- RUNX2 regulates genes involved in differentiation of myeloid cells
Biological Process
- monocyte chemotaxis
- mRNA processing
- RNA splicing
- neutrophil chemotaxis
- epithelial cell differentiation
Molecular Function
- RNA binding
- protein phosphatase inhibitor activity
- protein binding
- IgE binding
- protein phosphatase binding
Cellular Component
- immunological synapse
- extracellular region
- extracellular space
- nucleus
- spliceosomal complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000254301
- Coding exons
- 5
- Length
- 21299
- Individuals with no LoFs
- 124741
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 54
- Defined
- 124795
- p
- 0.000216
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.326 | 130 | 141 | 0.923 | 0.00000734 | 1582 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0.00046 | 0.00046 | rare |
| Ashkenazi Jewish | 0.00020 | 0.000099 | rare |
| East Asian | 0.00029 | 0.00028 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00012 | 0.00012 | rare |
| South Asian | 0.00036 | 0.00036 | rare |
| Other | 0.00083 | 0.00082 | rare |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.661
Intolerance Scores
- LoFtool
- 0.839
- RVIS EVS
- 0.93
- RVIS percentile EVS
- 89.7
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.490
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |