LGALS3BP
protein-codinggalectin 3 binding protein, the group of Receptor ligands|Scavenger receptor cysteine rich domain containing|BTB domain containing
Gene summary
The galectins are a family of beta-galactoside-binding proteins implicated in modulating cell-cell and cell-matrix interactions. LGALS3BP has been found elevated in the serum of patients with cancer and in those infected by the human immunodeficiency virus (HIV). It appears to be implicated in immune response associated with natural killer (NK) and lymphokine-activated killer (LAK) cell cytotoxicity. Using fluorescence in situ hybridization the full length 90K cDNA has been localized to chromosome 17q25. The native protein binds specifically to a human macrophage-associated lectin known as Mac-2 and also binds galectin 1. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.7 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 LGALS3BP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005567.4. 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 | 4 | 1 | 4 | 9 | ||
| missense | 81 | 6 | 1 | 88 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 86 | 7 | 5 | 98 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005558.1 | 5 | MANE Select | |
| Ensembl | ENSP00000262776.2 | 5 | MANE Select | |
| Ensembl | ENSP00000465729.1 | 4 | Standard | |
| Ensembl | ENSP00000465729.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Platelet degranulation
- Response to elevated platelet cytosolic Ca2+
- Platelet activation, signaling and aggregation
- Hemostasis
Biological Process
- platelet degranulation
- receptor-mediated endocytosis
- cellular defense response
- cell adhesion
- signal transduction
Molecular Function
- scavenger receptor activity
- protein binding
Cellular Component
- extracellular region
- extracellular space
- membrane
- platelet dense granule lumen
- collagen-containing extracellular matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262776
- Coding exons
- 5
- Length
- 8872
- Individuals with no LoFs
- 125583
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 140
- Defined
- 125723
- p
- 0.000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0771 | 341 | 345 | 0.988 | 0.0000203 | 3765 |
| Missense (PolyPhen) | 124 | 121.44 | 1.0211 | 1369 | ||
| Synonymous | 0.183 | 159 | 162 | 0.982 | 0.0000106 | 1210 |
| Loss of Function | 0.451 | 11 | 12.7 | 0.864 | 6.28e-7 | 133 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00055 | 0.00052 | rare |
| Ashkenazi Jewish | 0.0018 | 0.0018 | notable |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00063 | 0.00062 | rare |
| South Asian | 0.00077 | 0.00075 | rare |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Promotes integrin-mediated cell adhesion. May stimulate host defense against viruses and tumor cells. {ECO:0000269|PubMed:11146440, ECO:0000269|PubMed:8034587, ECO:0000269|PubMed:9501082}.;
Recessive Scores
- pRec
- 0.208
Intolerance Scores
- LoFtool
- 0.726
- RVIS EVS
- -0.97
- RVIS percentile EVS
- 8.9
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.890
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |