IL10RA

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

Basic information

Region (hg38): 11:117986370-118003037

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
IL10-related early-onset inflammatory bowel disease (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 (380 variants)
Inborn_genetic_diseases (60 variants)
not_provided (49 variants)
IL10RA-related_disorder (11 variants)
not_specified (5 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. These statistics are base on transcript: NM_000001558.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous		1 clinvar	5 clinvar	124 clinvar	4 clinvar	134
missense	6 clinvar	3 clinvar	182 clinvar	19 clinvar	2 clinvar	212
nonsense	5 clinvar	2 clinvar	1 clinvar			8
start loss	2					2
frameshift	4 clinvar					4
splice donor/acceptor (+/-2bp)	1 clinvar	1 clinvar				2
Total	18	7	188	143	6

Highest pathogenic variant AF is 0.0010996282

Loading clinvar variants...

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