IL10RB

interleukin 10 receptor subunit beta, the group of CD molecules|Interleukin receptors

Basic information

Region (hg38): 21:33266366-33311420

Previous symbols: [ "CRFB4", "D21S58", "D21S66" ]

Links

ENSG00000243646 ∙ NCBI:3588 ∙ OMIM:123889 ∙ HGNC:5965 ∙ Uniprot:Q08334 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• inflammatory bowel disease 25 (Strong), mode of inheritance: AR
• 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
Inflammatory bowel disease 25, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Allergy/Immunology/Infectious; Gastrointestinal	19890111; 21519361
HSCT has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL10RB gene.

• Inflammatory bowel disease 25 (204 variants)
• Inborn genetic diseases (13 variants)
• not provided (9 variants)
• not specified (6 variants)
• Inflammatory bowel disease (4 variants)
• Hepatitis B virus, susceptibility to;Inflammatory bowel disease 25 (3 variants)
• Inflammatory bowel disease 25;Hepatitis B virus, susceptibility to (1 variants)
• Hepatitis B virus, susceptibility to (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL10RB 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	43	2	46
missense			86	4	1	91
nonsense	4	1	1			6
start loss			2			2
frameshift		1	2			3
inframe indel			1			1
splice donor/acceptor (+/-2bp)		4				4
splice region			5	5	1	11
non coding			16	16	11	43
Total	4	6	109	63	14

Highest pathogenic variant AF is 0.0000131

Variants in IL10RB

This is a list of pathogenic ClinVar variants found in the IL10RB region.

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

Position	Type	Phenotype	Significance	ClinVar
21-33266372-C-A		Inflammatory bowel disease 25	Uncertain significance (Jan 13, 2018)
21-33266392-C-A		Inflammatory bowel disease 25	Uncertain significance (Jan 13, 2018)
21-33266394-C-A		Inflammatory bowel disease 25	Likely benign (Jan 13, 2018)
21-33266400-A-T		Inflammatory bowel disease 25	Uncertain significance (Jan 13, 2018)
21-33266466-A-C		Inflammatory bowel disease 25	Uncertain significance (Apr 08, 2021)
21-33266466-A-T		Inflammatory bowel disease 25	Uncertain significance (May 07, 2022)
21-33266470-C-T		Inflammatory bowel disease 25	Uncertain significance (Sep 19, 2022)
21-33266485-G-A		Inflammatory bowel disease 25	Uncertain significance (Feb 25, 2022)
21-33266486-C-T		Inflammatory bowel disease 25	Likely benign (Nov 19, 2019)
21-33266489-G-T		Inborn genetic diseases	Uncertain significance (Jul 22, 2022)
21-33266490-C-T		Inflammatory bowel disease 25	Likely benign (Dec 27, 2023)
21-33266492-G-A		Inflammatory bowel disease 25	Likely benign (Dec 09, 2022)
21-33266492-G-C		Inflammatory bowel disease 25	Likely benign (Sep 17, 2022)
21-33266494-G-C		Inflammatory bowel disease 25	Uncertain significance (Jan 18, 2022)
21-33266500-G-A		Inflammatory bowel disease 25	Uncertain significance (Aug 20, 2021)
21-33266504-G-A		Inflammatory bowel disease 25	Likely benign (Nov 17, 2023)
21-33266505-C-T		Inflammatory bowel disease 25	Likely benign (May 16, 2023)
21-33266516-T-G		Inflammatory bowel disease 25	Likely pathogenic (Jun 10, 2020)
21-33266519-G-A		Inflammatory bowel disease 25	Uncertain significance (Sep 12, 2022)
21-33266522-G-T		Inflammatory bowel disease 25 • IL10RB-related disorder	Likely benign (Apr 23, 2021)
21-33266526-G-A		Inflammatory bowel disease 25	Likely benign (Aug 28, 2023)
21-33266533-G-A		Inflammatory bowel disease 25	Likely benign (Aug 31, 2023)
21-33266533-G-T		Inflammatory bowel disease 25	Likely benign (Dec 01, 2021)
21-33266554-G-A		not specified	Benign (Nov 12, 2023)
21-33268374-T-C		Inflammatory bowel disease 25	Likely benign (Apr 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL10RB	protein_coding	protein_coding	ENST00000290200	7	30877

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000251	0.754	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.645	148	172	0.862	0.00000949	2158
Missense in Polyphen		24	38.826	0.61815		564
Synonymous	0.179	66	67.9	0.972	0.00000437	597
Loss of Function	1.22	11	16.3	0.674	7.76e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.000326	0.000326
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Shared cell surface receptor required for the activation of five class 2 cytokines: IL10, IL22, IL26, IL28, and IFNL1. The IFNLR1/IL10RB dimer is a receptor for the cytokine ligands IFNL2 and IFNL3 and mediates their antiviral activity. The ligand/receptor complex stimulate the activation of the JAK/STAT signaling pathway leading to the expression of IFN-stimulated genes (ISG), which contribute to the antiviral state. {ECO:0000269|PubMed:12469119, ECO:0000269|PubMed:15123776}.
• Disease: DISEASE: Inflammatory bowel disease 25 (IBD25) [MIM:612567]: A chronic, relapsing inflammation of the gastrointestinal tract with a complex etiology. It is subdivided into Crohn disease and ulcerative colitis phenotypes. Crohn disease may affect any part of the gastrointestinal tract from the mouth to the anus, but most frequently it involves the terminal ileum and colon. Bowel inflammation is transmural and discontinuous; it may contain granulomas or be associated with intestinal or perianal fistulas. In contrast, in ulcerative colitis, the inflammation is continuous and limited to rectal and colonic mucosal layers; fistulas and granulomas are not observed. Both diseases include extraintestinal inflammation of the skin, eyes, or joints. {ECO:0000269|PubMed:19890111}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);JAK-STAT-Core;Type III interferon signaling;Other interleukin signaling;Signaling by Interleukins;il-10 anti-inflammatory signaling pathway;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Interleukin-20 family signaling;Immune System;IL-10 signaling;Interleukin-10 signaling;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation (Consensus)

Recessive Scores

• pRec: 0.213

Intolerance Scores

• loftool: 0.558
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.0800
• hipred: N
• hipred_score: 0.139
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.865

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il10rb
• Phenotype: respiratory system phenotype; liver/biliary 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); hematopoietic system phenotype; digestive/alimentary phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: il10rb
• Affected structure: liver
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: inflammatory response;immune response;signal transduction;cytokine-mediated signaling pathway;defense response to virus
• Cellular component: plasma membrane;integral component of membrane;interleukin-28 receptor complex
• Molecular function: cytokine receptor activity;interleukin-10 receptor activity;protein binding;signaling receptor activity