IL13
interleukin 13, the group of Interleukins
Basic information
Region (hg38): 5:132656263-132661110
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 IL13 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 | 1 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 3 | 2 | 3 |
Variants in IL13
This is a list of pathogenic ClinVar variants found in the IL13 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-132657117-C-T | Inherited susceptibility to asthma | risk factor (May 15, 2005) | ||
| 5-132658194-C-T | not specified | Likely benign (Dec 13, 2022) | ||
| 5-132658305-C-G | not specified | Uncertain significance (Jun 05, 2023) | ||
| 5-132658339-C-A | Benign (Aug 16, 2018) | |||
| 5-132659734-C-T | not specified | Uncertain significance (May 11, 2022) | ||
| 5-132659799-G-A | not specified | Uncertain significance (Jun 10, 2024) | ||
| 5-132660166-G-T | IL13-related disorder | Likely benign (Jul 01, 2019) | ||
| 5-132660197-G-A | IL13-related disorder | Benign (Nov 07, 2019) | ||
| 5-132660267-G-T | not specified | Uncertain significance (Mar 05, 2024) | ||
| 5-132660272-A-G | Inherited susceptibility to asthma • Allergic rhinitis, susceptibility to • IL13-related disorder | Benign; risk factor (Oct 16, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IL13 | protein_coding | protein_coding | ENST00000304506 | 4 | 4848 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0144 | 0.697 | 125328 | 0 | 3 | 125331 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.373 | 75 | 84.7 | 0.886 | 0.00000471 | 939 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000883 | 0.00000883 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
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.;
- Pathway
- 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);IL-17 signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Measles - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Fc Epsilon Receptor I Signaling in Mast Cells;JAK-STAT-Core;Allograft Rejection;Lung fibrosis;Development and heterogeneity of the ILC family;Cytokines and Inflammatory Response;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Interleukin-4 and 13 signaling;Signaling by Interleukins;gata3 participate in activating the th2 cytokine genes expression;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;IL12 signaling mediated by STAT4;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Immune System;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;Glucocorticoid receptor regulatory network;JAK STAT pathway and regulation;IL4;GPCR signaling-G alpha i;IL-13 signaling
(Consensus)
Recessive Scores
- pRec
- 0.0692
Intolerance Scores
- loftool
- 0.548
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.32
Haploinsufficiency Scores
- pHI
- 0.242
- hipred
- N
- hipred_score
- 0.257
- ghis
- 0.421
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.202
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Il13
- Phenotype
- respiratory system phenotype; hematopoietic system phenotype; 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); reproductive system phenotype; digestive/alimentary phenotype; 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); immune system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- microglial cell activation;positive regulation of immunoglobulin production;inflammatory response;immune response;regulation of proton transport;regulation of signaling receptor activity;positive regulation of gene expression;cytokine-mediated signaling pathway;positive regulation of B cell proliferation;response to lipopolysaccharide;positive regulation of connective tissue growth factor production;negative regulation of NAD(P)H oxidase activity;response to nicotine;positive regulation of tyrosine phosphorylation of STAT protein;positive regulation of macrophage activation;positive regulation of mast cell degranulation;response to ethanol;positive regulation of smooth muscle cell proliferation;positive regulation of protein secretion;positive regulation of release of sequestered calcium ion into cytosol;cellular response to mechanical stimulus;negative regulation of transforming growth factor beta production;positive regulation of cold-induced thermogenesis;negative regulation of neuron death;negative regulation of lung ciliated cell differentiation;positive regulation of lung goblet cell differentiation;negative regulation of complement-dependent cytotoxicity;positive regulation of pancreatic stellate cell proliferation;negative regulation of endothelial cell apoptotic process
- Cellular component
- extracellular region;extracellular space;cytoplasm;external side of plasma membrane
- Molecular function
- cytokine activity;interleukin-13 receptor binding;protein binding