IL9
Basic information
Region (hg38): 5:135892246-135895841
Links
Phenotypes
GenCC
Source:
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 IL9 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 | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 1 | 0 |
Variants in IL9
This is a list of pathogenic ClinVar variants found in the IL9 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-135892431-A-T | not specified | Uncertain significance (Dec 01, 2022) | ||
| 5-135892432-A-G | not specified | Uncertain significance (Jun 18, 2024) | ||
| 5-135892446-C-G | not specified | Uncertain significance (May 23, 2023) | ||
| 5-135892461-A-G | not specified | Uncertain significance (Mar 16, 2022) | ||
| 5-135892464-G-A | not specified | Uncertain significance (Dec 06, 2021) | ||
| 5-135892466-G-A | Likely benign (Aug 28, 2018) | |||
| 5-135892477-T-C | not specified | Uncertain significance (Nov 17, 2022) | ||
| 5-135894037-T-G | not specified | Uncertain significance (Feb 01, 2023) | ||
| 5-135894061-C-T | not specified | Uncertain significance (Feb 28, 2024) | ||
| 5-135894064-G-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 5-135894084-C-G | not specified | Uncertain significance (May 27, 2022) | ||
| 5-135894120-C-A | not specified | Uncertain significance (Mar 01, 2024) | ||
| 5-135895433-T-C | Likely benign (Feb 08, 2018) | |||
| 5-135895770-A-G | not specified | Uncertain significance (Aug 02, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IL9 | protein_coding | protein_coding | ENST00000274520 | 5 | 3582 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 8.11e-7 | 0.0926 | 125530 | 0 | 213 | 125743 | 0.000847 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.253 | 70 | 76.2 | 0.918 | 0.00000363 | 944 |
| Missense in Polyphen | 26 | 23.704 | 1.0969 | 289 | ||
| Synonymous | -0.224 | 32 | 30.4 | 1.05 | 0.00000169 | 273 |
| Loss of Function | -0.898 | 8 | 5.69 | 1.41 | 2.39e-7 | 71 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000183 | 0.000181 |
| Ashkenazi Jewish | 0.000199 | 0.000198 |
| East Asian | 0.00881 | 0.00885 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000159 | 0.000158 |
| Middle Eastern | 0.00881 | 0.00885 |
| South Asian | 0.000823 | 0.000817 |
| Other | 0.000327 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Supports IL-2 independent and IL-4 independent growth of helper T-cells.;
- Pathway
- Jak-STAT signaling pathway - Homo sapiens (human);Asthma - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;IL-9 Signaling Pathway;Development and heterogeneity of the ILC family;T-Cell antigen Receptor (TCR) Signaling Pathway;Signaling by Interleukins;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Interleukin-9 signaling;Immune System;Interleukin-2 family signaling;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;GPCR signaling-G alpha i
(Consensus)
Recessive Scores
- pRec
- 0.280
Intolerance Scores
- loftool
- 0.732
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.11
Haploinsufficiency Scores
- pHI
- 0.0555
- hipred
- N
- hipred_score
- 0.123
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.631
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Il9
- Phenotype
- homeostasis/metabolism phenotype; immune system phenotype; digestive/alimentary phenotype; normal phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- inflammatory response;immune response;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of cell growth;interleukin-9-mediated signaling pathway;positive regulation of interleukin-5 biosynthetic process
- Cellular component
- extracellular region;extracellular space
- Molecular function
- cytokine activity;interleukin-9 receptor binding;growth factor activity