IL15
interleukin 15, the group of Interleukins
Basic information
Region (hg38): 4:141636583-141733987
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 IL15 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 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 8 | 1 | 1 |
Variants in IL15
This is a list of pathogenic ClinVar variants found in the IL15 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-141720478-T-G | not specified | Uncertain significance (Jan 19, 2024) | ||
| 4-141721962-G-T | not specified | Uncertain significance (Jan 11, 2023) | ||
| 4-141727962-T-C | not specified | Uncertain significance (Dec 27, 2023) | ||
| 4-141727975-T-G | not specified | Uncertain significance (Apr 25, 2022) | ||
| 4-141727982-C-T | not specified | Uncertain significance (Jul 12, 2023) | ||
| 4-141729955-C-T | Benign (Jul 16, 2018) | |||
| 4-141729967-A-C | not specified | Uncertain significance (Dec 07, 2022) | ||
| 4-141732767-T-C | Likely benign (Aug 03, 2017) | |||
| 4-141732789-A-T | not specified | Uncertain significance (Jan 08, 2024) | ||
| 4-141732795-G-C | not specified | Uncertain significance (Feb 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IL15 | protein_coding | protein_coding | ENST00000296545 | 6 | 97389 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.709 | 0.288 | 106645 | 0 | 1 | 106646 | 0.00000469 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0747 | 79 | 80.9 | 0.977 | 0.00000364 | 1086 |
| Missense in Polyphen | 24 | 27.638 | 0.86836 | 407 | ||
| Synonymous | 1.08 | 20 | 27.1 | 0.737 | 0.00000132 | 275 |
| Loss of Function | 2.36 | 1 | 8.36 | 0.120 | 4.40e-7 | 103 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000481 | 0.0000481 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cytokine that stimulates the proliferation of T- lymphocytes. Stimulation by IL-15 requires interaction of IL-15 with components of IL-2R, including IL-2R beta and probably IL-2R gamma but not IL-2R alpha.;
- Pathway
- Jak-STAT signaling pathway - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);JAK-STAT-Core;Development and heterogeneity of the ILC family;Cytokines and Inflammatory Response;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;Immune System;Interleukin-15 signaling;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;IL2;GPCR signaling-G alpha i
(Consensus)
Recessive Scores
- pRec
- 0.595
Intolerance Scores
- loftool
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 62.74
Haploinsufficiency Scores
- pHI
- 0.157
- hipred
- Y
- hipred_score
- 0.594
- ghis
- 0.497
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.454
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Il15
- Phenotype
- renal/urinary system phenotype; immune system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- natural killer cell differentiation;NK T cell proliferation;inflammatory response;immune response;signal transduction;tyrosine phosphorylation of STAT protein;cell-cell signaling;aging;positive regulation of cell population proliferation;regulation of signaling receptor activity;skeletal muscle atrophy;hyaluronan metabolic process;positive regulation of interleukin-17 production;positive regulation of natural killer cell proliferation;positive regulation of natural killer cell differentiation;positive regulation of tissue remodeling;interleukin-15-mediated signaling pathway;positive regulation of T cell proliferation;positive regulation of tyrosine phosphorylation of STAT protein;extrathymic T cell selection;regulation of T cell differentiation;cell maturation;lymph node development;negative regulation of smooth muscle cell proliferation;regulation of defense response to virus by host;positive regulation of inflammatory response;positive regulation of immune response;cellular response to vitamin D;negative regulation of cold-induced thermogenesis;positive regulation of protein O-linked glycosylation
- Cellular component
- extracellular region;extracellular space;nucleoplasm;cytoplasm;endosome;Golgi apparatus;cytosol;cell surface;nuclear speck
- Molecular function
- cytokine activity;cytokine receptor binding;protein binding