IL15

interleukin 15, the group of Interleukins

Basic information

Region (hg38): 4:141636582-141733987

Links

ENSG00000164136 ∙ NCBI:3600 ∙ OMIM:600554 ∙ HGNC:5977 ∙ Uniprot:P40933 ∙ 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 IL15 gene.

• Inborn genetic diseases (5 variants)
• not provided (2 variants)

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				1	1	2
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	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: gnomAD

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: dbNSFP

• 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

• 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_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