IL2RB

interleukin 2 receptor subunit beta, the group of CD molecules|Interleukin receptors

Basic information

Region (hg38): 22:37118665-37175118

Previous symbols: [ "IL15RB" ]

Links

ENSG00000100385 ∙ NCBI:3560 ∙ OMIM:146710 ∙ HGNC:6009 ∙ Uniprot:P14784 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency 63 with lymphoproliferation and autoimmunity (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 63 with lymphoproliferation and autoimmunity	AR	Allergy/Immunology/Infectious	Individuals have been described with immunodeficiency and immune dysregulation; immune suppression has been described as being beneficial prior to HSCT	Allergy/Immunology/Infectious; Gastrointestinal	31040184; 31040185

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL2RB gene.

• not provided (296 variants)
• Inborn genetic diseases (17 variants)
• not specified (10 variants)
• Immunodeficiency 63 with lymphoproliferation and autoimmunity (8 variants)
• IL2RB-related condition (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL2RB 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	82	3	86
missense			128	7	6	141
nonsense	2		1			3
start loss						0
frameshift			3			3
inframe indel			1			1
splice donor/acceptor (+/-2bp)		5	1			6
splice region			5	13	3	21
non coding			1	31	11	43
Total	2	5	136	120	20

Highest pathogenic variant AF is 0.00000657

Variants in IL2RB

This is a list of pathogenic ClinVar variants found in the IL2RB region.

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

Position	Type	Phenotype	Significance	ClinVar
22-37128100-A-G		not specified	Uncertain significance (Jul 07, 2023)
22-37128113-G-A			Uncertain significance (Mar 05, 2022)
22-37128117-C-T			Likely benign (Sep 09, 2023)
22-37128121-C-T			Uncertain significance (Nov 27, 2021)
22-37128154-G-A			Uncertain significance (Jun 09, 2022)
22-37128164-G-A			Uncertain significance (Feb 08, 2022)
22-37128169-C-T		not specified	Uncertain significance (Aug 11, 2022)
22-37128170-G-A			Uncertain significance (Oct 17, 2022)
22-37128182-C-T			Uncertain significance (Aug 06, 2022)
22-37128198-C-G			Likely benign (Jul 11, 2022)
22-37128201-A-C			Likely benign (Dec 21, 2022)
22-37128205-G-A		not specified	Uncertain significance (Oct 30, 2023)
22-37128211-GACCAGGGGAA-G			Uncertain significance (May 28, 2021)
22-37128216-G-T			Likely benign (Jul 12, 2023)
22-37128217-G-A			Uncertain significance (Jun 22, 2022)
22-37128226-A-C			Uncertain significance (May 14, 2022)
22-37128228-T-G			Likely benign (Nov 14, 2020)
22-37128233-C-T			Uncertain significance (Sep 06, 2022)
22-37128240-G-A			Likely benign (Dec 25, 2023)
22-37128246-G-A			Likely benign (Jun 04, 2023)
22-37128251-G-A			Uncertain significance (May 25, 2022)
22-37128254-C-A			Uncertain significance (Aug 16, 2021)
22-37128257-C-G			Uncertain significance (May 09, 2022)
22-37128257-C-T			Uncertain significance (Jun 09, 2022)
22-37128261-C-T			Likely benign (Jan 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL2RB	protein_coding	protein_coding	ENST00000216223	9	49217

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.291	0.709	125666	2	80	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.441	284	306	0.929	0.0000172	3527
Missense in Polyphen		54	77.591	0.69596		966
Synonymous	0.180	139	142	0.981	0.00000899	1151
Loss of Function	3.26	5	21.2	0.236	0.00000101	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00168	0.00168
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00359	0.00326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for interleukin-2. This beta subunit is involved in receptor mediated endocytosis and transduces the mitogenic signals of IL2.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Endocytosis - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Measles - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Inflammatory Response Pathway;IL-2 Signaling Pathway;Signaling by GPCR;Signal Transduction;Signaling by Interleukins;il 2 signaling pathway;il-2 receptor beta chain in t cell activation;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Immune System;Interleukin-15 signaling;Interleukin receptor SHC signaling;Interleukin-2 family signaling;IL-2 signaling;SHP2 signaling;JAK STAT MolecularVariation 2;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;JAK STAT pathway and regulation;IL2;IL2-mediated signaling events;Interleukin-2 signaling;IL5;G beta:gamma signalling through PI3Kgamma;G-protein beta:gamma signalling;GPCR downstream signalling;IL2 signaling events mediated by STAT5;Downstream signaling in naïve CD8+ T cells;IL2 signaling events mediated by PI3K;IL12-mediated signaling events;Interleukin-3, 5 and GM-CSF signaling (Consensus)

Recessive Scores

• pRec: 0.509

Intolerance Scores

• loftool: 0.112
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.91

Haploinsufficiency Scores

• pHI: 0.535
• hipred: Y
• hipred_score: 0.671
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.339

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il2rb
• Phenotype: immune system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; hematopoietic system phenotype; growth/size/body region phenotype; 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); 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); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: MAPK cascade;signal transduction;viral process;cytokine-mediated signaling pathway;interleukin-15-mediated signaling pathway;interleukin-2-mediated signaling pathway;negative regulation of apoptotic process;protein-containing complex assembly
• Cellular component: endosome;cytosol;plasma membrane;integral component of plasma membrane;external side of plasma membrane;membrane
• Molecular function: interleukin-2 receptor activity;Ras guanyl-nucleotide exchange factor activity;protein binding;interleukin-2 binding