IL23R

interleukin 23 receptor

Basic information

Region (hg38): 1:67138907-67259979

Links

ENSG00000162594 ∙ NCBI:149233 ∙ OMIM:607562 ∙ HGNC:19100 ∙ Uniprot:Q5VWK5 ∙ 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 IL23R gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL23R 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			2	64	7	73
missense			138	5	5	148
nonsense			1			1
start loss						0
frameshift			5			5
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			7	17	1	25
non coding			1	35	7	43
Total	0	0	147	104	19

Variants in IL23R

This is a list of pathogenic ClinVar variants found in the IL23R region.

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

Position	Type	Phenotype	Significance	ClinVar
1-67168128-A-G			Uncertain significance (Nov 07, 2023)
1-67168129-G-T		not specified	Benign (Feb 01, 2024)
1-67168142-TG-T			Uncertain significance (Dec 04, 2022)
1-67168147-T-G			Uncertain significance (Oct 04, 2023)
1-67168148-G-A			Uncertain significance (May 07, 2023)
1-67168159-C-T			Likely benign (Aug 23, 2022)
1-67168166-A-G			Uncertain significance (Aug 27, 2022)
1-67168175-A-G		not specified	Uncertain significance (Jan 02, 2024)
1-67168178-T-C			Uncertain significance (Oct 06, 2023)
1-67168179-G-T			Uncertain significance (Jul 17, 2023)
1-67168191-G-GTA			Uncertain significance (Sep 11, 2023)
1-67168195-GGT-G			Likely benign (Sep 29, 2022)
1-67168196-G-A			Uncertain significance (Jul 19, 2023)
1-67168206-T-C			Likely benign (Jul 31, 2023)
1-67168210-T-A			Likely benign (Jan 16, 2024)
1-67169358-C-T			Likely benign (Sep 16, 2022)
1-67169369-A-G		not specified	Uncertain significance (Jan 18, 2022)
1-67169370-C-T			Likely benign (Oct 16, 2022)
1-67169371-A-C			Uncertain significance (Aug 31, 2021)
1-67169375-G-A			Uncertain significance (Jan 12, 2023)
1-67169376-G-T			Uncertain significance (Aug 31, 2022)
1-67169377-G-A			Uncertain significance (Dec 06, 2022)
1-67169382-A-G			Likely benign (Nov 12, 2021)
1-67169393-T-A			Uncertain significance (Aug 04, 2023)
1-67169419-A-G			Uncertain significance (Dec 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL23R	protein_coding	protein_coding	ENST00000347310	10	93580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000560	0.999	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	264	318	0.829	0.0000145	4173
Missense in Polyphen		48	79.053	0.60718		928
Synonymous	-0.0174	114	114	1.00	0.00000579	1141
Loss of Function	3.22	11	30.0	0.366	0.00000136	377

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with IL12RB1 to form the interleukin-23 receptor. Binds IL23 and mediates T-cells, NK cells and possibly certain macrophage/myeloid cells stimulation probably through activation of the Jak-Stat signaling cascade. IL23 functions in innate and adaptive immunity and may participate in acute response to infection in peripheral tissues. IL23 may be responsible for autoimmune inflammatory diseases and be important for tumorigenesis. {ECO:0000269|PubMed:12023369}.
• Disease: DISEASE: Inflammatory bowel disease 17 (IBD17) [MIM:612261]: 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:17068223, ECO:0000269|PubMed:17804789}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Inflammatory bowel disease (IBD) - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Interleukin-4 and 13 signaling;Interleukin-12 family signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Immune System;Interleukin-23 signaling;IL23-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.331

Intolerance Scores

• loftool: 0.367
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.49

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il23r
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; immune system phenotype; digestive/alimentary phenotype; hematopoietic system phenotype; neoplasm

Gene ontology

• Biological process: positive regulation of T cell mediated cytotoxicity;positive regulation of defense response to virus by host;positive regulation of T-helper 1 type immune response;inflammatory response;positive regulation of activation of Janus kinase activity;cytokine-mediated signaling pathway;response to lipopolysaccharide;negative regulation of interleukin-10 production;positive regulation of granulocyte macrophage colony-stimulating factor production;positive regulation of interferon-gamma production;positive regulation of interleukin-12 production;positive regulation of interleukin-17 production;positive regulation of natural killer cell proliferation;response to interferon-gamma;interleukin-23-mediated signaling pathway;positive regulation of T cell proliferation;positive regulation of activated T cell proliferation;regulation of tyrosine phosphorylation of STAT protein;positive regulation of tyrosine phosphorylation of STAT protein;positive regulation of memory T cell differentiation;positive regulation of osteoclast differentiation;defense response to Gram-negative bacterium;positive regulation of NK T cell activation;positive regulation of T-helper 17 type immune response;positive regulation of T-helper 17 cell lineage commitment
• Cellular component: plasma membrane;external side of plasma membrane;receptor complex;interleukin-23 receptor complex
• Molecular function: cytokine receptor activity;interleukin-12 receptor binding;protein binding;cytokine binding;interleukin-23 binding;interleukin-23 receptor activity