LGALS13
protein-codinggalectin 13, the group of Galectins
Gene summary
Lysophospholipases are enzymes that act on biological membranes to regulate the multifunctional lysophospholipids. The protein encoded by this gene has lysophospholipase activity. It is composed of two identical subunits which are held together by disulfide bonds. This protein has structural similarity to several members of the beta-galactoside-binding S-type lectin family. [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 ~5.0 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 LGALS13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013268.3. 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 | 0 | |||||
| missense | 16 | 1 | 17 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 16 | 1 | 0 | 17 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_037400.1 | 4 | MANE Select | |
| Ensembl | ENSP00000221797.3 | 4 | MANE Select | |
| Ensembl | ENSP00000470928.1 | 3 | Standard | |
| Ensembl | ENSP00000774034.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- phospholipid metabolic process
- apoptotic process
- positive regulation of T cell apoptotic process
Molecular Function
- lysophospholipase activity
- protein binding
- carbohydrate binding
Cellular Component
- cytoplasm
- nuclear matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000221797
- Coding exons
- 4
- Length
- 4953
- Individuals with no LoFs
- 125407
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 337
- Defined
- 125747
- p
- 0.00135
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.208 | 85 | 79.8 | 1.07 | 0.00000467 | 912 |
| Missense (PolyPhen) | 34 | 23.739 | 1.4322 | 318 | ||
| Synonymous | -1.17 | 39 | 30.7 | 1.27 | 0.00000190 | 258 |
| Loss of Function | 0.598 | 5 | 6.67 | 0.750 | 4.47e-7 | 61 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.018 | 0.018 | notable |
| Latino/Admixed American | 0.00084 | 0.00084 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00015 | 0.00015 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Binds beta-galactoside and lactose. Strong inducer of T- cell apoptosis (PubMed:10527825, PubMed:19497882). Has hemagglutinating activity towards chicken erythrocytes (PubMed:29343868). {ECO:0000269|PubMed:10527825, ECO:0000269|PubMed:19497882, ECO:0000269|PubMed:29343868}.;
Recessive Scores
- pRec
- 0.158
Intolerance Scores
- LoFtool
- 0.753
- RVIS EVS
- 0.57
- RVIS percentile EVS
- 81.99
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.486
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |