IL23A
interleukin 23 subunit alpha, the group of Interleukins
Basic information
Region (hg38): 12:56334173-56340410
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL23A 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 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 1 |
Variants in IL23A
This is a list of pathogenic ClinVar variants found in the IL23A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-56339426-G-C | not specified | Uncertain significance (Nov 09, 2023) | ||
| 12-56339462-G-A | not specified | Uncertain significance (May 04, 2022) | ||
| 12-56339746-C-T | not specified | Uncertain significance (Jul 25, 2023) | ||
| 12-56339747-G-A | not specified | Benign (Mar 29, 2016) | ||
| 12-56339766-C-G | not specified | Uncertain significance (Mar 16, 2022) | ||
| 12-56340006-C-T | not specified | Uncertain significance (Nov 21, 2023) | ||
| 12-56340007-G-A | not specified | Uncertain significance (Nov 09, 2021) | ||
| 12-56340063-G-A | not specified | Uncertain significance (Dec 07, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IL23A | protein_coding | protein_coding | ENST00000228534 | 4 | 1531 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.358 | 0.631 | 125740 | 0 | 6 | 125746 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.19 | 67 | 101 | 0.665 | 0.00000512 | 1219 |
| Missense in Polyphen | 28 | 41.105 | 0.68118 | 441 | ||
| Synonymous | 1.30 | 28 | 38.2 | 0.733 | 0.00000173 | 393 |
| Loss of Function | 2.13 | 2 | 8.86 | 0.226 | 3.79e-7 | 93 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000124 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000165 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Associates with IL12B to form the IL-23 interleukin, a heterodimeric cytokine which functions in innate and adaptive immunity. IL-23 may constitute with IL-17 an acute response to infection in peripheral tissues. IL-23 binds to a heterodimeric receptor complex composed of IL12RB1 and IL23R, activates the Jak- Stat signaling cascade, stimulates memory rather than naive T- cells and promotes production of proinflammatory cytokines. IL-23 induces autoimmune inflammation and thus may be responsible for autoimmune inflammatory diseases and may be important for tumorigenesis. {ECO:0000269|PubMed:11114383, ECO:0000269|PubMed:12023369, ECO:0000269|PubMed:16424222}.;
- Pathway
- Pertussis - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Inflammatory bowel disease (IBD) - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Development and heterogeneity of the ILC family;Interleukin-12 family signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Immune System;ATF-2 transcription factor network;Interleukin-23 signaling;IL23-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.583
Intolerance Scores
- loftool
- 0.270
- rvis_EVS
- -0.08
- rvis_percentile_EVS
- 47.79
Haploinsufficiency Scores
- pHI
- 0.384
- hipred
- N
- hipred_score
- 0.491
- ghis
- 0.594
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.929
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Il23a
- Phenotype
- homeostasis/metabolism 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); immune system phenotype; digestive/alimentary 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); 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;regulation of signaling receptor activity;positive regulation of activation of Janus kinase activity;cytokine-mediated signaling pathway;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-10 production;positive regulation of interleukin-12 production;positive regulation of interleukin-17 production;positive regulation of tumor necrosis factor production;positive regulation of natural killer cell activation;positive regulation of natural killer cell proliferation;positive regulation of tissue remodeling;interleukin-23-mediated signaling pathway;T cell proliferation;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;innate immune response;positive regulation of osteoclast differentiation;positive regulation of transcription by RNA polymerase II;tissue remodeling;positive regulation of inflammatory response;defense response to Gram-negative bacterium;positive regulation of NK T cell activation;positive regulation of NK T cell proliferation;defense response to virus;positive regulation of neutrophil chemotaxis;positive regulation of NIK/NF-kappaB signaling;positive regulation of T-helper 17 type immune response;positive regulation of T-helper 17 cell lineage commitment
- Cellular component
- extracellular region;endoplasmic reticulum lumen;interleukin-23 complex
- Molecular function
- cytokine activity;protein binding;interleukin-23 receptor binding