IL4

interleukin 4, the group of Interleukins

Basic information

Region (hg38): 5:132673985-132682678

Links

ENSG00000113520 ∙ NCBI:3565 ∙ OMIM:147780 ∙ HGNC:6014 ∙ Uniprot:P05112 ∙ 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 IL4 gene.

• Inborn genetic diseases (5 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL4 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			4			4
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	1

Variants in IL4

This is a list of pathogenic ClinVar variants found in the IL4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-132679748-C-T		not specified	Uncertain significance (Aug 02, 2021)
5-132679793-G-A		not specified	Uncertain significance (Feb 13, 2024)
5-132679820-T-C		not specified	Uncertain significance (Jun 22, 2021)
5-132679831-A-C		not specified	Uncertain significance (Feb 28, 2023)
5-132679853-A-C		not specified	Uncertain significance (Jan 23, 2023)
5-132679861-G-A		not specified	Uncertain significance (Nov 10, 2022)
5-132679863-C-T			Benign (Dec 31, 2019)
5-132679879-C-G		not specified	Uncertain significance (Nov 14, 2023)
5-132682550-C-T		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL4	protein_coding	protein_coding	ENST00000231449	4	8691

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00474	0.702	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.348	80	89.2	0.896	0.00000534	1002
Missense in Polyphen		29	40.2	0.72139		457
Synonymous	-0.434	44	40.5	1.09	0.00000269	295
Loss of Function	0.701	4	5.82	0.687	2.47e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000277	0.000277
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in at least several B-cell activation processes as well as of other cell types (PubMed:3016727). It is a costimulator of DNA-synthesis. It induces the expression of class II MHC molecules on resting B-cells. It enhances both secretion and cell surface expression of IgE and IgG1. It also regulates the expression of the low affinity Fc receptor for IgE (CD23) on both lymphocytes and monocytes. Positively regulates IL31RA expression in macrophages (By similarity). Stimulates autophagy in dendritic cells by interfering with mTORC1 signaling and through the induction of RUFY4 (By similarity). {ECO:0000250|UniProtKB:P07750, ECO:0000269|PubMed:3016727}.
• Disease: DISEASE: Ischemic stroke (ISCHSTR) [MIM:601367]: A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors. {ECO:0000269|PubMed:14681304}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);Fc epsilon RI signaling pathway - Homo sapiens (human);Allograft rejection - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Autoimmune thyroid disease - Homo sapiens (human);Inflammatory bowel disease (IBD) - Homo sapiens (human);Asthma - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Measles - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Fc Epsilon Receptor I Signaling in Mast Cells;JAK-STAT-Core;Folate Metabolism;Allograft Rejection;Spinal Cord Injury;Lung fibrosis;T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection;IL-4 Signaling Pathway;Development and heterogeneity of the ILC family;PI3K-Akt Signaling Pathway;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Inflammatory Response Pathway;Cytokines and Inflammatory Response;Interleukin-4 and 13 signaling;Signaling by Interleukins;gata3 participate in activating the th2 cytokine genes expression;il 4 signaling pathway;the 41bb-dependent immune response;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;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;IL-4 signaling;Glucocorticoid receptor regulatory network;JAK STAT pathway and regulation;Notch signaling pathway;IL4;GPCR signaling-G alpha i;IL2 signaling events mediated by STAT5;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;AP-1 transcription factor network;IL4-mediated signaling events;IL12-mediated signaling events;Calcium signaling in the CD4+ TCR pathway;IL-13 signaling (Consensus)

Recessive Scores

• pRec: 0.852

Intolerance Scores

• loftool: 0.618
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.218
• hipred: N
• hipred_score: 0.182
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.788

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Il4
• 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); digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; respiratory system phenotype; liver/biliary system phenotype; reproductive 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); normal phenotype; hematopoietic system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism 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)

Gene ontology

• Biological process: immune response;cholesterol metabolic process;regulation of signaling receptor activity;positive regulation of gene expression;negative regulation of epithelial cell migration;positive regulation of macroautophagy;cytokine-mediated signaling pathway;B cell differentiation;positive regulation of B cell proliferation;positive regulation of interleukin-13 production;T-helper 2 cell cytokine production;type 2 immune response;positive regulation of T cell proliferation;T cell activation;regulation of phosphorylation;positive regulation of tyrosine phosphorylation of STAT protein;activation of Janus kinase activity;myeloid dendritic cell differentiation;negative regulation of apoptotic process;connective tissue growth factor biosynthetic process;regulation of isotype switching;positive regulation of MHC class II biosynthetic process;positive regulation of T cell differentiation;negative regulation of osteoclast differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of isotype switching to IgE isotypes;positive regulation of isotype switching to IgG isotypes;regulation of immune response;dendritic cell differentiation;positive regulation of cold-induced thermogenesis;negative regulation of complement-dependent cytotoxicity;negative regulation of endothelial cell apoptotic process
• Cellular component: extracellular region;extracellular space
• Molecular function: cytokine activity;interleukin-4 receptor binding;protein binding;growth factor activity