IL13
protein-codinginterleukin 13, the group of Interleukins
Gene summary
This gene encodes an immunoregulatory cytokine produced primarily by activated Th2 cells. This cytokine is involved in several stages of B-cell maturation and differentiation. It up-regulates CD23 and MHC class II expression, and promotes IgE isotype switching of B cells. This cytokine down-regulates macrophage activity, thereby inhibits the production of pro-inflammatory cytokines and chemokines. This cytokine is found to be critical to the pathogenesis of allergen-induced asthma but operates through mechanisms independent of IgE and eosinophils. This gene, IL3, IL5, IL4, and CSF2 form a cytokine gene cluster on chromosome 5q, with this gene particularly close to IL4. [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 ~4.8 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 IL13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002188.3. 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 | 1 | 1 | ||||
| missense | 8 | 2 | 1 | 11 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 8 | 2 | 2 | 12 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002179.2 | 4 | MANE Select | |
| Ensembl | ENSP00000304915.3 | 4 | MANE Select | |
| RefSeq | NP_001341920.1 | 3 | Standard | |
| RefSeq | NP_001341921.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Fc epsilon RI signaling pathway - Homo sapiens (human)
- Jak-STAT signaling pathway - Homo sapiens (human)
- Inflammatory bowel disease (IBD) - Homo sapiens (human)
- Asthma - Homo sapiens (human)
- Th1 and Th2 cell differentiation - Homo sapiens (human)
Biological Process
- microglial cell activation
- positive regulation of immunoglobulin production
- inflammatory response
- immune response
- regulation of proton transport
Molecular Function
- cytokine activity
- interleukin-13 receptor binding
- protein binding
Cellular Component
- extracellular region
- extracellular space
- cytoplasm
- external side of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000304506
- Coding exons
- 4
- Length
- 4848
- Individuals with no LoFs
- 125328
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125331
- p
- 0.0000120
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.373 | 75 | 84.7 | 0.886 | 0.00000471 | 939 |
| Missense (PolyPhen) | 20 | 24.711 | 0.80935 | 311 | ||
| Synonymous | 0.910 | 31 | 38.2 | 0.813 | 0.00000256 | 298 |
| Loss of Function | 0.622 | 3 | 4.41 | 0.680 | 1.86e-7 | 55 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Cytokine (PubMed:8096327, PubMed:8097324). Inhibits inflammatory cytokine production (PubMed:8096327). Synergizes with IL2 in regulating interferon-gamma synthesis (PubMed:8096327). May be critical in regulating inflammatory and immune responses (PubMed:8096327, PubMed:8097324). Positively regulates IL31RA expression in macrophages (By similarity). {ECO:0000250|UniProtKB:P20109, ECO:0000269|PubMed:8096327, ECO:0000269|PubMed:8097324}.;
- Disease
- DISEASE: Allergic rhinitis (ALRH) [MIM:607154]: A common disease with complex inheritance characterized by mucosal inflammation caused by allergen exposure. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.0692
Intolerance Scores
- LoFtool
- 0.548
- RVIS EVS
- 0.15
- RVIS percentile EVS
- 64.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.202
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |