IL2RB

protein-coding

interleukin 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]

Previous symbols:
  • IL15RB

MANE transcript

NM_000878.5

Inheritance

AR

ClinVar variants

P:14U:210B:163

Top phenotype

Immunodeficiency 63 with lymphoproliferation and autoimmunity

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr22:37,118,666-37,175,118

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~56.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

immunodeficiency 63 with lymphoproliferation and autoimmunitySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032782

Submitter: Labcorp Genetics (formerly Invitae)

immunodeficiency 63 with lymphoproliferation and autoimmunityMODERATE

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).

immunodeficiency 63 with lymphoproliferation and autoimmunitySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032782

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Immunodeficiency 63 with lymphoproliferation and autoimmunityAR

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

Refs: 31040184; 31040185Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IL2RB variants in ClinVar

5 Conditions Cataloged
not providedTotal: 436
not specifiedTotal: 117
IL2RB-related disorderTotal: 16
Immunodeficiency 63 with lymphoproliferation and autoimmunityTotal: 7
IchthyosisTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
139
clinvar
2
clinvar
146
missense
2
clinvar
198
clinvar
19
clinvar
3
clinvar
222
nonsense
4
clinvar
2
clinvar
6
start loss
0
frameshift
1
clinvar
3
clinvar
4
splice donor/acceptor (+/-2bp)
7
clinvar
2
clinvar
9
Total772101585387

Highest pathogenic variant AF is 0.000013146651

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000878.5RefSeqNP_000869.19MANE Select
ENST00000216223.10EnsemblENSP00000216223.59MANE Select
NM_001346222.1RefSeqNP_001333151.19Standard
NM_001346223.2RefSeqNP_001333152.19Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4412843060.9290.00001723527
Missense (PolyPhen)5477.5910.69596966
Synonymous0.1801391420.9810.000008991151
Loss of Function3.26521.20.2360.00000101213

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.00160.0016notable
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000440.000044rare
South Asian00.0absent
Other0.00360.0033notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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