IL15RA

interleukin 15 receptor subunit alpha, the group of CD molecules|Sushi domain containing|Interleukin receptors

Basic information

Region (hg38): 10:5943639-5978187

Links

ENSG00000134470 ∙ NCBI:3601 ∙ OMIM:601070 ∙ HGNC:5978 ∙ Uniprot:Q13261 ∙ 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 IL15RA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL15RA 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				3		3
missense			15	4	3	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	7	3

Variants in IL15RA

This is a list of pathogenic ClinVar variants found in the IL15RA region.

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

Position	Type	Phenotype	Significance	ClinVar
10-5953149-A-G			Likely benign (Mar 01, 2023)
10-5953184-C-T			Benign (Apr 04, 2018)
10-5953195-G-A		not specified	Uncertain significance (Apr 08, 2022)
10-5953199-G-A		not specified	Likely benign (Jan 17, 2024)
10-5956406-G-A		not specified	Uncertain significance (Jan 17, 2024)
10-5956410-C-T		not specified	Uncertain significance (Jun 07, 2023)
10-5956442-G-A		not specified	Uncertain significance (Sep 13, 2023)
10-5960405-T-G			Benign (Feb 18, 2020)
10-5960426-G-C		not specified	Uncertain significance (Mar 28, 2024)
10-5960437-G-C			Benign/Likely benign (Mar 01, 2023)
10-5960442-A-G		not specified	Likely benign (Sep 06, 2023)
10-5960444-T-C		not specified	Uncertain significance (Oct 16, 2023)
10-5960507-G-A		not specified	Uncertain significance (Aug 20, 2023)
10-5960529-C-T		not specified	Uncertain significance (Mar 08, 2024)
10-5960531-G-A		not specified	Likely benign (Mar 24, 2023)
10-5960534-G-A		not specified	Uncertain significance (Oct 29, 2021)
10-5960550-G-A		not specified	Likely benign (Nov 17, 2023)
10-5963761-G-A		not specified	Uncertain significance (Jun 10, 2024)
10-5963764-T-C		not specified	Uncertain significance (Dec 13, 2021)
10-5963793-G-A			Benign (Jul 06, 2018)
10-5963811-G-A		not specified	Likely benign (Jun 18, 2024)
10-5963815-G-A		not specified	Uncertain significance (Feb 21, 2024)
10-5966186-G-A		not specified	Uncertain significance (Jan 02, 2024)
10-5966190-C-A		not specified	Uncertain significance (Dec 27, 2023)
10-5966226-C-T		not specified	Uncertain significance (May 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL15RA	protein_coding	protein_coding	ENST00000379977	7	29296

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000233	0.299	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.229	139	147	0.947	0.00000860	1678
Missense in Polyphen		86	84.161	1.0218		914
Synonymous	0.179	65	66.9	0.972	0.00000475	587
Loss of Function	0.233	9	9.79	0.920	4.15e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.00	0.00
South Asian	0.000197	0.000196
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: High-affinity receptor for interleukin-15. Can signal both in cis and trans where IL15R from one subset of cells presents IL15 to neighboring IL2RG-expressing cells. Expression of different isoforms may alter or interfere with signal transduction. Isoform 5, isoform 6, isoform 7 and isoform 8 do not bind IL15. Signal transduction involves SYK. {ECO:0000269|PubMed:11714793, ECO:0000269|PubMed:8530383}.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);JAK-STAT-Core;T-Cell antigen Receptor (TCR) Signaling Pathway;Signaling by Interleukins;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Immune System;Interleukin-15 signaling;Interleukin-2 family signaling;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.884
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.0368
• hipred: N
• hipred_score: 0.214
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0157

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il15ra
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: signal transduction;cell population proliferation;interleukin-15-mediated signaling pathway
• Cellular component: Golgi membrane;extracellular space;endosome;endoplasmic reticulum membrane;plasma membrane;integral component of membrane;cytoplasmic vesicle membrane;nuclear membrane
• Molecular function: cytokine receptor activity;protein binding