IL13

interleukin 13, the group of Interleukins

Basic information

Region (hg38): 5:132656262-132661110

Links

ENSG00000169194 ∙ NCBI:3596 ∙ OMIM:147683 ∙ HGNC:5973 ∙ Uniprot:P35225 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL13 gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

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	1
missense			2	1		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	1	1

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)
5-132660166-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 (Oct 16, 2019)

GnomAD

Source: gnomAD

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: dbNSFP

• 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