IL2RA

protein-coding

interleukin 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]

Previous symbols:
  • IL2R
  • IDDM10

MANE transcript

NM_000417.3

Inheritance

AR

ClinVar variants

P:16U:132B:73

Top phenotype

Immunodeficiency 41 with lymphoproliferation and autoimmunity

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr10:6,010,689-6,062,370

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~51.7 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neonatal diabetes mellitus with congenital hypothyroidismSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012436

Submitter: Genomics England PanelApp

immunodeficiency due to CD25 deficiencyDEFINITIVE

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.

immunodeficiency due to CD25 deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011664

Submitter: Labcorp Genetics (formerly Invitae)

immunodeficiency due to CD25 deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011664

Submitter: PanelApp Australia

immunodeficiency due to CD25 deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0011664

Submitter: Orphanet

type 1 diabetes mellitus 10STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0011168

Submitter: Genomics England PanelApp

neonatal diabetes mellitusSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0016391

Submitter: Genomics England PanelApp

Clinical Genomic Database (CGD)

Immunodeficiency 41 with lymphoproliferation and autoimmunityAR

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

Refs: 9096364; 10879793Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IL2RA variants in ClinVar

7 Conditions Cataloged
Immunodeficiency due to CD25 deficiencyTotal: 270
not specifiedTotal: 50
not providedTotal: 30
Type 1 diabetes mellitus 10Total: 5
IL2RA-related disorderTotal: 3
Pleural effusionTotal: 1
MyelodysplasiaTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
65
clinvar
1
clinvar
68
missense
2
clinvar
1
clinvar
125
clinvar
6
clinvar
1
clinvar
135
nonsense
4
clinvar
1
clinvar
5
start loss
1
clinvar
1
frameshift
2
clinvar
2
splice donor/acceptor (+/-2bp)
2
clinvar
4
clinvar
4
clinvar
10
Total106132712221

Highest pathogenic variant AF is 0.000015054037

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000417.3RefSeqNP_000408.18MANE Select
ENST00000379959.8EnsemblENSP00000369293.38MANE Select
NM_001308242.2RefSeqNP_001295171.17Standard
NM_001308243.2RefSeqNP_001295172.16Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.3621451580.9190.000008961801
Missense (PolyPhen)3443.1180.78854512
Synonymous-0.8446456.01.140.00000377482
Loss of Function2.55516.00.3136.92e-7187

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian0.000160.00016rare
Finnish00.0absent
European (Non-Finnish)0.0000260.000026rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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