IL2RB
protein-codinginterleukin 2 receptor subunit beta, the group of CD molecules|Interleukin receptors
Gene summary
The interleukin 2 receptor, which is involved in T cell-mediated immune responses, is present in 3 forms with respect to ability to bind interleukin 2. The low affinity form is a monomer of the alpha subunit and is not involved in signal transduction. The intermediate affinity form consists of an alpha/beta subunit heterodimer, while the high affinity form consists of an alpha/beta/gamma subunit heterotrimer. Both the intermediate and high affinity forms of the receptor are involved in receptor-mediated endocytosis and transduction of mitogenic signals from interleukin 2. The protein encoded by this gene represents the beta subunit and is a type I membrane protein. The use of alternative promoters results in multiple transcript variants encoding the same protein. The protein is primarily expressed in the hematopoietic system. The use by some variants of an alternate promoter in an upstream long terminal repeat (LTR) results in placenta-specific expression. [provided by RefSeq, Sep 2016]
- IL15RB
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~56.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0032782
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0032782
Submitter: ClinGen
IL2RB deficiency was first reported as the cause of autosomal recessive immunodeficiency 63 with lymphoproliferation and autoimmune disease in 2019 (Fernadez et al., PMID: 31040184). Patients with this disorder have a susceptibility to herpesvirus infections as well as severe autoimmune and inflammatory disease in the form of autoimmune haemolytic anaemia, enteropathy, dermatitis, hypergammaglobulinemia, lymphadenopathy and splenomegaly. Four variants (missense and nonsense) that have been reported in 5 probands in 2 publications (PMIDs: 31040184, 31040185) are included in this curation. Variants in this gene segregated with disease in 5 additional family members. The heterozygous parents all appear unaffected. A further case is available as a poster abstract (https://doi.org/10.1136/flgastro-2021-bspghan.33) that was unable to be scored, however personal correspondence confirmed the patient shared the same variant (L77P) as reported in two of the scored probands (PMID: 31040185). The mechanism of pathogenicity appears to be loss of function. Autosomal recessive immunodeficiency 63 with lymphoproliferation and autoimmune disease is caused by partial or complete biallelic loss of function of IL2RB resulting in impaired IL-2 and IL-15 signaling, immune dysregulation and autoimmunity. This gene-disease relationship is supported by animal models, expression studies, functional studies and rescue in animal and patient cells (PMIDs: 23352221, 1631559, 8026467, 10706676, 7770771, 31040185). IL2RB encodes the beta subunit of the IL-2 and IL-15 receptors, and is expressed on resting T cells, NK cells, monocytes and neutrophils. The expression and function of IL2RB is reviewed by Liao et al (2013). There are many studies examining the function and expression of IL2RB, and both IL-2 and IL-15 are important in lymphocyte development and regulation. Suzuki et al (1995) first described the Il2rb -/- mouse which displays some phenotypic similarities to that of humans with IL2RB deficiency including lethal autoimmune disease and lymphoproliferation. Further studies on this mouse demonstrated that either thymic IL2RB expression or adoptive transfer of T regulatory cells (CD4+CD25+) was sufficient to rescue the autoimmune immunophenotype (Malek et al., 2000). Finally, transduction of affected patient cells with IL-2RB partially restores deficient IL-2 signaling (Zhang et al., 2019). In summary, there is moderate evidence supporting the relationship between IL2RB and autosomal recessive immunodeficiency 63 with lymphoproliferation and autoimmune disease. This evidence has been reported in both research and clinical diagnostic settings, and has been upheld over time, though at the time of this curation, only 5 probands have been reported in two publications. This classification was approved by the ClinGen PIRD GCEP on the meeting date December 12, 2023 (SOP Version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0032782
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Gastrointestinal
Intervention: Allergy/Immunology/Infectious
Rationale: Individuals have been described with immunodeficiency and immune dysregulation; immune suppression has been described as being beneficial prior to HSCT
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to IL2RB variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000878.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 5 | 139 | 2 | 146 | ||
| missense | 2 | 198 | 19 | 3 | 222 | |
| nonsense | 4 | 2 | 6 | |||
| start loss | 0 | |||||
| frameshift | 1 | 3 | 4 | |||
| splice donor/acceptor (+/-2bp) | 7 | 2 | 9 | |||
| Total | 7 | 7 | 210 | 158 | 5 | 387 |
Highest pathogenic variant AF is 0.000013146651
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000869.1 | 9 | MANE Select | |
| Ensembl | ENSP00000216223.5 | 9 | MANE Select | |
| RefSeq | NP_001333151.1 | 9 | Standard | |
| RefSeq | NP_001333152.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- MAPK cascade
- signal transduction
- viral process
- cytokine-mediated signaling pathway
- interleukin-15-mediated signaling pathway
Molecular Function
- interleukin-2 receptor activity
- Ras guanyl-nucleotide exchange factor activity
- protein binding
- interleukin-2 binding
Cellular Component
- endosome
- cytosol
- plasma membrane
- integral component of plasma membrane
- external side of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000216223
- Coding exons
- 9
- Length
- 49217
- Individuals with no LoFs
- 125666
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 80
- Defined
- 125748
- p
- 0.000326
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.441 | 284 | 306 | 0.929 | 0.0000172 | 3527 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.0016 | 0.0016 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.0036 | 0.0033 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Receptor for interleukin-2. This beta subunit is involved in receptor mediated endocytosis and transduces the mitogenic signals of IL2.;
Recessive Scores
- pRec
- 0.509
Intolerance Scores
- LoFtool
- 0.112
- RVIS EVS
- 0.44
- RVIS percentile EVS
- 77.91
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.339
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |