IL10

interleukin 10, the group of Interleukins

Basic information

Region (hg38): 1:206767601-206774541

Links

ENSG00000136634 ∙ NCBI:3586 ∙ OMIM:124092 ∙ HGNC:5962 ∙ Uniprot:P22301 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Graft vs. host disease	AD	Pharmacogenomic	In Graft vs. host disease, variants may have clinical relevance, as specific allele(s) shown to be a marker of favorable outcome following transplantation	General	14657422; 14657427; 20305143

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL10 gene.

• Inflammatory bowel disease (98 variants)
• not specified (5 variants)
• not provided (3 variants)
• Inborn genetic diseases (2 variants)
• Leprosy, susceptibility to, 1 (1 variants)
• Graft-versus-host disease, resistance to (1 variants)
• Susceptibility to HIV infection (1 variants)
• Graft-versus-host disease, susceptibility to;Susceptibility to HIV infection;Rheumatoid arthritis (1 variants)
• Cholangiocarcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL10 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				28		28
missense			43	1		44
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			3	3	1	7
non coding				10	10	20
Total	0	0	45	39	10

Variants in IL10

This is a list of pathogenic ClinVar variants found in the IL10 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-206768519-A-G		not specified	Benign (Nov 12, 2023)
1-206768639-G-C		Inflammatory bowel disease	Uncertain significance (Oct 18, 2022)
1-206768639-G-T		Inflammatory bowel disease	Uncertain significance (May 25, 2022)
1-206768643-C-T		Inflammatory bowel disease	Uncertain significance (Apr 07, 2022)
1-206768644-G-A		Inflammatory bowel disease	Uncertain significance (Jul 09, 2022)
1-206768652-A-G		Inflammatory bowel disease	Uncertain significance (Aug 31, 2021)
1-206768659-T-C		Inflammatory bowel disease	Uncertain significance (Aug 01, 2023)
1-206768660-G-A		Inflammatory bowel disease	Likely benign (Nov 19, 2018)
1-206768663-G-A		Inflammatory bowel disease	Likely benign (Sep 13, 2022)
1-206768666-T-G		Inflammatory bowel disease	Uncertain significance (Aug 31, 2021)
1-206768670-A-T		Inflammatory bowel disease	Uncertain significance (May 27, 2022)
1-206768671-T-C		Inflammatory bowel disease	Uncertain significance (Apr 17, 2021)
1-206768702-G-A		Inflammatory bowel disease	Likely benign (Sep 06, 2023)
1-206768702-G-T		Inflammatory bowel disease	Likely benign (Dec 25, 2019)
1-206768736-G-A		Inflammatory bowel disease	Likely benign (Nov 29, 2023)
1-206769809-C-T		Inflammatory bowel disease	Likely benign (Dec 30, 2023)
1-206769812-C-T		Inflammatory bowel disease	Likely benign (Mar 07, 2023)
1-206769821-A-G		Inflammatory bowel disease	Likely benign (Jun 24, 2023)
1-206769823-G-A		Inflammatory bowel disease	Uncertain significance (Jun 25, 2022)
1-206769830-T-C		Inflammatory bowel disease	Uncertain significance (Jun 14, 2022)
1-206769839-G-A		Inflammatory bowel disease	Uncertain significance (Aug 30, 2021)
1-206769849-C-G		Inflammatory bowel disease	Uncertain significance (Jan 03, 2023)
1-206769859-G-C		Inflammatory bowel disease	Likely benign (Jul 19, 2022)
1-206769880-G-A		Inflammatory bowel disease	Likely benign (Feb 20, 2019)
1-206769887-A-T		Inflammatory bowel disease	Uncertain significance (Feb 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL10	protein_coding	protein_coding	ENST00000423557	5	4893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00589	0.912	125739	0	7	125746	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.841	71	93.9	0.756	0.00000492	1188
Missense in Polyphen		14	33.425	0.41885		449
Synonymous	-0.0174	36	35.9	1.00	0.00000176	322
Loss of Function	1.49	5	10.1	0.494	6.63e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000361	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T-cells.
• Pathway: T cell receptor signaling pathway - Homo sapiens (human);Pertussis - Homo sapiens (human);Allograft rejection - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Systemic lupus erythematosus - Homo sapiens (human);Autoimmune thyroid disease - Homo sapiens (human);Inflammatory bowel disease (IBD) - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);African trypanosomiasis - Homo sapiens (human);Asthma - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Malaria - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);Staphylococcus aureus infection - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);JAK-STAT-Core;Allograft Rejection;T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection;Interleukin-4 and 13 signaling;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;PI3K-AKT-mTOR - VitD3 Signalling;Cytokines and Inflammatory Response;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Signaling by Interleukins;il-10 anti-inflammatory signaling pathway;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Immune System;IL-10 signaling;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;Interleukin-10 signaling;JAK STAT pathway and regulation;GPCR signaling-G alpha i;AP-1 transcription factor network;IL4-mediated signaling events;Regulation of nuclear SMAD2/3 signaling (Consensus)

Recessive Scores

• pRec: 0.945

Intolerance Scores

• loftool: 0.538
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.473
• hipred: N
• hipred_score: 0.353
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.962

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il10
• Phenotype: skeleton phenotype; immune system phenotype; vision/eye phenotype; digestive/alimentary phenotype; limbs/digits/tail 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); neoplasm; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; normal 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); liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; muscle phenotype; endocrine/exocrine gland 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)

Gene ontology

• Biological process: positive regulation of endothelial cell proliferation;response to molecule of bacterial origin;negative regulation of cytokine secretion involved in immune response;negative regulation of chronic inflammatory response to antigenic stimulus;positive regulation of B cell apoptotic process;inflammatory response;cytoplasmic sequestering of NF-kappaB;aging;negative regulation of cell population proliferation;regulation of gene expression;response to activity;response to inactivity;cytokine-mediated signaling pathway;hemopoiesis;B cell differentiation;leukocyte chemotaxis;negative regulation of myeloid dendritic cell activation;negative regulation of B cell proliferation;negative regulation of interferon-gamma production;negative regulation of interleukin-1 production;negative regulation of interleukin-12 production;negative regulation of interleukin-18 production;negative regulation of interleukin-6 production;negative regulation of interleukin-8 production;negative regulation of tumor necrosis factor production;receptor biosynthetic process;response to insulin;negative regulation of heterotypic cell-cell adhesion;positive regulation of heterotypic cell-cell adhesion;response to carbon monoxide;interleukin-12-mediated signaling pathway;cellular response to hepatocyte growth factor stimulus;type 2 immune response;B cell proliferation;negative regulation of T cell proliferation;negative regulation of tumor necrosis factor biosynthetic process;defense response to bacterium;defense response to protozoan;positive regulation of macrophage activation;negative regulation of apoptotic process;negative regulation of growth of symbiont in host;negative regulation of nitric oxide biosynthetic process;regulation of isotype switching;negative regulation of MHC class II biosynthetic process;positive regulation of MHC class II biosynthetic process;negative regulation of interferon-alpha biosynthetic process;positive regulation of cell cycle;positive regulation of transcription, DNA-templated;negative regulation of mitotic cell cycle;positive regulation of cytokine secretion;negative regulation of inflammatory response;regulation of synapse organization;negative regulation of membrane protein ectodomain proteolysis;positive regulation of DNA-binding transcription factor activity;response to glucocorticoid;negative regulation of cytokine activity;branching involved in labyrinthine layer morphogenesis;cellular response to lipopolysaccharide;cellular response to estradiol stimulus;negative regulation of chemokine (C-C motif) ligand 5 production;endothelial cell apoptotic process;liver regeneration;positive regulation of pri-miRNA transcription by RNA polymerase II;regulation of response to wounding;negative regulation of hydrogen peroxide-induced neuron death;regulation of complement-dependent cytotoxicity;positive regulation of sprouting angiogenesis;negative regulation of sensory perception of pain;negative regulation of vascular smooth muscle cell proliferation;positive regulation of vascular smooth muscle cell proliferation;negative regulation of endothelial cell apoptotic process
• Cellular component: extracellular region;extracellular space
• Molecular function: cytokine activity;interleukin-10 receptor binding;protein binding;growth factor activity