IL10RA

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

Basic information

Region (hg38): 11:117986369-118003037

Previous symbols: [ "IL10R" ]

Links

ENSG00000110324 ∙ NCBI:3587 ∙ OMIM:146933 ∙ HGNC:5964 ∙ Uniprot:Q13651 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• inflammatory bowel disease 28 (Moderate), mode of inheritance: AR
• immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections syndrome (Supportive), mode of inheritance: AR
• inflammatory bowel disease 28 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Inflammatory bowel disease 28, 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; 22476154

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL10RA gene.

• Inflammatory bowel disease 28 (357 variants)
• not provided (41 variants)
• Inborn genetic diseases (14 variants)
• not specified (11 variants)
• IL10RA-related condition (3 variants)
• Inflammatory bowel disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL10RA 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			5	82	7	94
missense	3	2	143	10	5	163
nonsense	3	2	2			7
start loss						0
frameshift	3					3
inframe indel			3			3
splice donor/acceptor (+/-2bp)		1				1
splice region		1	4	3		8
non coding			26	30	9	65
Total	9	5	179	122	21

Highest pathogenic variant AF is 0.0000328

Variants in IL10RA

This is a list of pathogenic ClinVar variants found in the IL10RA region.

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

Position	Type	Phenotype	Significance	ClinVar
11-117986398-C-T		Inflammatory bowel disease 28	Likely benign (Jan 13, 2018)
11-117986403-C-T		Inflammatory bowel disease 28	Uncertain significance (Apr 27, 2017)
11-117986414-T-C		Inflammatory bowel disease 28	Uncertain significance (Jan 13, 2018)
11-117986439-C-T		Inflammatory bowel disease 28	Uncertain significance (Jan 13, 2018)
11-117986465-AGGATGCTGCCGTGCCTCGTAGTGCTGCTGGCGGCGCTCCTCAGCCTCCGTCTTGGCTCAGACGCTCAT-A		Inflammatory bowel disease 28	Pathogenic (Feb 25, 2021)
11-117986475-C-A		Inflammatory bowel disease 28	Likely benign (Jan 31, 2024)
11-117986475-C-G		Inflammatory bowel disease 28	Uncertain significance (Jun 20, 2019)
11-117986480-C-T		Inflammatory bowel disease 28	Uncertain significance (Sep 11, 2023)
11-117986483-G-C		Inflammatory bowel disease 28	Uncertain significance (Aug 24, 2021)
11-117986484-T-C		Inflammatory bowel disease 28	Uncertain significance (Jun 04, 2022)
11-117986487-T-A		Inflammatory bowel disease 28	Uncertain significance (Dec 06, 2019)
11-117986488-G-A		Inflammatory bowel disease 28	Likely benign (Jan 20, 2020)
11-117986488-G-C		not specified • Inflammatory bowel disease 28	Benign/Likely benign (Apr 01, 2024)
11-117986492-C-T		Inflammatory bowel disease 28	Uncertain significance (Jan 13, 2018)
11-117986497-G-A		Inflammatory bowel disease 28	Likely benign (Jul 15, 2022)
11-117986504-C-T		Inflammatory bowel disease 28	Uncertain significance (Aug 15, 2022)
11-117986511-T-C		Inflammatory bowel disease 28	Uncertain significance (Jun 12, 2022)
11-117986512-C-T		Inflammatory bowel disease 28	Likely benign (Apr 06, 2021)
11-117986513-C-T		Inflammatory bowel disease 28	Uncertain significance (Oct 01, 2022)
11-117986514-G-C		Inflammatory bowel disease 28 • Inborn genetic diseases	Uncertain significance (Oct 27, 2023)
11-117986532-A-C		Inflammatory bowel disease 28	Uncertain significance (Feb 07, 2022)
11-117986540-G-T		Inflammatory bowel disease 28	Uncertain significance (Aug 31, 2021)
11-117986542-T-C		Inflammatory bowel disease 28	Conflicting classifications of pathogenicity (Jan 29, 2024)
11-117986542-T-G		IL10RA-related disorder	Likely benign (Nov 08, 2023)
11-117986544-C-T		Inflammatory bowel disease 28	Conflicting classifications of pathogenicity (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL10RA	protein_coding	protein_coding	ENST00000227752	7	15134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0178	0.978	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.637	286	318	0.900	0.0000176	3766
Missense in Polyphen		47	63.939	0.73507		819
Synonymous	-0.600	144	135	1.07	0.00000760	1194
Loss of Function	2.52	6	17.3	0.347	0.00000102	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for IL10; binds IL10 with a high affinity.
• 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;TYROBP Causal Network;Signaling by Interleukins;il22 soluble receptor signaling pathway;il-10 anti-inflammatory signaling pathway;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Immune System;IL-10 signaling;Interleukin-10 signaling;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation (Consensus)

Recessive Scores

• pRec: 0.407

Intolerance Scores

• loftool: 0.137
• rvis_EVS: 0.98
• rvis_percentile_EVS: 90.43

Haploinsufficiency Scores

• pHI: 0.192
• hipred: N
• hipred_score: 0.455
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.923

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il10ra
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; hematopoietic system phenotype; immune system phenotype; digestive/alimentary phenotype

Zebrafish Information Network

• Gene name: il10ra
• Affected structure: response to cytokine
• Phenotype tag: abnormal
• Phenotype quality: decreased process quality

Gene ontology

• Biological process: cytokine-mediated signaling pathway;response to lipopolysaccharide;regulation of synapse organization
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: cytokine receptor activity;interleukin-10 receptor activity;protein binding;interleukin-10 binding;signaling receptor activity