IL2RA
protein-codinginterleukin 2 receptor subunit alpha, the group of CD molecules|Sushi domain containing|Interleukin receptors
Gene summary
The interleukin 2 (IL2) receptor alpha (IL2RA) and beta (IL2RB) chains, together with the common gamma chain (IL2RG), constitute the high-affinity IL2 receptor. Homodimeric alpha chains (IL2RA) result in low-affinity receptor, while homodimeric beta (IL2RB) chains produce a medium-affinity receptor. Normally an integral-membrane protein, soluble IL2RA has been isolated and determined to result from extracellular proteolyisis. Alternately-spliced IL2RA mRNAs have been isolated, but the significance of each is presently unknown. Mutations in this gene are associated with interleukin 2 receptor alpha deficiency. Patients with severe Coronavirus Disease 2019 (COVID-19), the disease caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have significantly elevated levels of IL2R in their plasma. Similarly, serum IL-2R levels are found to be elevated in patients with different types of carcinomas. Certain IL2RA and IL2RB gene polymorphisms have been associated with lung cancer risk. [provided by RefSeq, Jul 2020]
- IL2R
- IDDM10
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~51.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0012436
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0011664
Submitter: ClinGen
*IL2RA* was first reported in relation to autosomal recessive immunodeficiency due to CD25 deficiency in 1997 (Sharfe et al., PMID: 9096364). This disease is a complex disorder of immune dysregulation. Affected individuals present in infancy with recurrent viral, fungal, and bacterial infections, lymphadenopathy, and variable autoimmune features, such as autoimmune enteropathy and eczematous skin lesions. Immunologic studies show a defect in T-cell regulation (OMIM:606367). Thirteen unique variants (missense, splicing, nonsense and frameshift) reported in nine probands in nine publications (PMIDs: 9096364, 17196245, 23416241, 24116927, 35968218, 36195682, 29995861, 30742970, 31605764) are included in this curation. Immunodeficiency presented early (>1mo to 7mo) in all probands with various phenotypes including but not limited to chronic diarrhea, enlarged lymphoid tissues, and eczema. More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. The mechanism of pathogenicity is suspected to be loss of function. This gene-disease relationship is also supported by experimental evidence (expression, functional, functional alteration, and animal models. *IL2RA* encodes CD25, which is part of interleukin-2-mediated signaling pathway (PMID: 16293754) resulting in a defect in IL-2 signaling in patient CD4+ T cells (PMID: 23416241). Expression is concentrated in lymphoid tissues (PMID: 25613900). One mouse model showed *IL2RA* defective mice developing autoimmunity deficiencies, and similarly defective lymphoid tissue development (PMID: 7584142). In summary, there is definitive evidence supporting the relationship between *IL2RA* and autosomal recessive immunodeficiency due to CD25 deficiency. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen PIRD GCEP on the meeting date November 21, 2023 (SOP Version 11). **The following amendment was approved by the Monogenic Diabetes GCEP April 30, 2025** Biallelic pathogenic variants in IL2RA are a rare cause of autosomal recessive IL2RA (AKA CD25) deficiency that often presents in infancy with recurrent viral, fungal, and bacterial infections, lymphadenopathy, and variable autoimmune IPEX-like features, such as autoimmune enteropathy and eczematous skin lesions, as well as diabetes, which has often been described as a feature. Of 15 reported cases, diabetes was described as the presenting feature in 6 cases (6/15 = 40%) (PMID:17196245, 29995861, 29329106, 31605764, 38408297). When diabetes was the presenting feature, it occurred at very young ages (2 days – 15 weeks of age), suggesting that genetic testing for neonatal diabetes is an important path leading to diagnosis of this rare condition. Diabetes was described as an additional non-presenting feature in 3 additional cases (PMID:29183106, 31605764, 35662751), suggesting that diabetes is present in more than half of affected IL2RA cases (9/15 = 60%). In many cases scant clinical details were provided, but most suggested that the diabetes was insulin-requiring. In addition, several of the cases were found to have positive diabetes-specific antibodies, providing further evidence of the likely autoimmune etiology of the diabetes in this rare condition characterized by immunodysregulation. Finding biallelic P/LP variants in IL2RA in individuals with diabetes should prompt for awareness and/or screening for immune and lymphoproliferative dysfunction as well as other autoimmune problems. Similarly, in individuals discovered to have P/LP IL2RA variants but who have not been diagnosed with diabetes, glucose monitoring is advised, based on the ~60% prevalence of diabetes in this disorder.
Inheritance Pattern: AR
Disease ID:MONDO:0011664
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0011664
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0011664
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0011168
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0016391
Submitter: Genomics England PanelApp
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Gastrointestinal
Intervention: Allergy/Immunology/Infectious
Rationale: Described individuals have an increased susceptibility to bacterial, fungal, and viral infections, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial; BMT has been described
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to IL2RA variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000417.3. 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 | 2 | 65 | 1 | 68 | ||
| missense | 2 | 1 | 125 | 6 | 1 | 135 |
| nonsense | 4 | 1 | 5 | |||
| start loss | 1 | 1 | ||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 4 | 4 | 10 | ||
| Total | 10 | 6 | 132 | 71 | 2 | 221 |
Highest pathogenic variant AF is 0.000015054037
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000408.1 | 8 | MANE Select | |
| Ensembl | ENSP00000369293.3 | 8 | MANE Select | |
| RefSeq | NP_001295171.1 | 7 | Standard | |
| RefSeq | NP_001295172.1 | 6 | 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
- inflammatory response to antigenic stimulus
- regulation of T cell tolerance induction
- apoptotic process
- activation-induced cell death of T cells
Molecular Function
- interleukin-2 receptor activity
- Ras guanyl-nucleotide exchange factor activity
- protein binding
- interleukin-2 binding
Cellular Component
- plasma membrane
- external side of plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000379959
- Coding exons
- 8
- Length
- 51637
- Individuals with no LoFs
- 125738
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 125746
- p
- 0.0000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.362 | 145 | 158 | 0.919 | 0.00000896 | 1801 |
| Missense (PolyPhen) | 34 | 43.118 | 0.78854 | 512 | ||
| Synonymous | -0.844 | 64 | 56.0 | 1.14 | 0.00000377 | 482 |
| Loss of Function | 2.55 | 5 | 16.0 | 0.313 | 6.92e-7 | 187 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000026 | 0.000026 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Receptor for interleukin-2. The receptor is involved in the regulation of immune tolerance by controlling regulatory T cells (TREGs) activity. TREGs suppress the activation and expansion of autoreactive T-cells. {ECO:0000269|PubMed:23416241, ECO:0000269|PubMed:24116927}.;
- Disease
- DISEASE: Diabetes mellitus, insulin-dependent, 10 (IDDM10) [MIM:601942]: A multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical features are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269|PubMed:17676041}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Immunodeficiency 41 with lymphoproliferation and autoimmunity (IMD41) [MIM:606367]: A disorder of immune dysregulation characterized by recurrent viral, fungal, and bacterial infections, lymphadenopathy, and variable autoimmune features, such as autoimmune enteropathy and eczematous skin lesions. {ECO:0000269|PubMed:23416241, ECO:0000269|PubMed:24116927}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.695
Intolerance Scores
- LoFtool
- 0.493
- RVIS EVS
- -0.6
- RVIS percentile EVS
- 17.75
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.566
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |