• Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top tube
  • Alternate specimens:
    DNA or saliva/assisted saliva
  • Sample requirements
  • Request a sample kit




Associated disorders

The IL2RG gene is associated with X-linked recessive severe combined immunodeficiency (MedGen UID: 220906).

An estimated 20% – 28% of severe combined immunodeficiency (SCID) is caused by pathogenic variants identified in IL2RG (PMID: 8410508, 25138334).

The IL2RG gene encodes the common gamma chain which is a subunit for several receptors that are important for lymphocyte development and function. Upon ligand binding to the IL2 receptor, the gamma subunit interacts with the JAK3 tyrosine kinase to transduce the signal (PMID: 26235889).

X-linked severe combined immunodeficiency (X-SCID)
MedGen UID: 220906

Clinical condition
X-linked severe combined immunodeficiency (X-SCID) is a disorder of profound impairment in cellular and humoral immunity caused by pathogenic variants in the IL2RG gene (PMID: 9058718). If not recognized during the neonatal period (either through newborn screening or due to a family history), males with X-SCID come to medical attention at 3-6 months of age when maternal antibody levels diminish, and affected infants experience severe bacterial, fungal, and viral infections, and failure to thrive (PMID: 25937517). Infections are recurrent, persistent, and life threatening. Presenting symptoms often include absent tonsils and lymph nodes, chronic diarrhea, fevers, sepsis, and pneumonia (PMID: 28747913, 25937517). The immunophenotype of X-SCID is characterized by near absent T cells, low or absent natural killer (NK) cells, and normal or increased numbers of nonfunctional B cells (T-, B+, NK-; PMID: 20301584).

A milder form of IL2RG-related SCID is known as atypical or “leaky” X-SCID. Leaky SCID is characterized by the presence of T and B cells with little or absent NK cells and is caused by hypomorphic mutations in IL2RG (PMID: 20301584, 25138334). Symptoms of leaky SCID include infantile-onset immune dysregulation, rashes, splenomegaly, gastrointestinal malabsorption, and poor growth (PMID: 18559672, 17598841, 25042067). Like typical SCID, leaky SCID can also be fatal if left untreated (PMID: 20301584).

Revertant somatic mosaicism, in which a pathogenic allele is spontaneously corrected, has been reported in several males with atypical late-onset X-SCID (PMID: 26407811).
In 2008, state newborn screening programs began screening for SCID, enabling early identification of babies requiring further clinical evaluation. SCID is currently included in the newborn screening programs of 44 states, and 4 additional states have pilot programs (Immune Deficiency Foundation. http://primaryimmune.org. Accessed August 2017). In the US, over 95% of infants are covered by newborn screening protocols, which identify individuals with SCID by measurement of low T-cell receptor excision circles (TREC; PMID: 22285280 ). Clinical evaluation and molecular testing is used to confirm newborn screening results. Early identification of asymptomatic infants by newborn screening and subsequent treatment with hematopoietic cell transplant (HCT) or gene therapy results in significantly improved outcomes (PMID: 25937517, 26235889).

The incidence of SCID is estimated to be 1 in 58,000 based on newborn screening data (PMID: 25138334). X-SCID is the most common form of severe combined immunodeficiency (PMID: 25138334).

Differential diagnosis
SCID is an infantile-onset primary immunodeficiency syndrome that results in T-lymphocyte and B-lymphocyte dysfunction. Some subtypes of SCID may also result in defective NK cell function. Flow cytometry results may inform the subtype of SCID; however different genetic subtypes have the same lymphocyte subset profile, and several forms of SCID share a clinical presentation. An infant with HIV may present similarly to an infant with SCID; however, T cells are generally present in those with HIV (PMID: 20301584). An abnormal SCID newborn screen can be indicative of other genetic syndromes, including 22q11.2 deletion syndrome, Jacobsen syndrome, Trisomy 21, and CHARGE syndrome, as well as other non-genetic conditions including extreme prematurity, congenital heart defects, and intrauterine growth retardation (PMID: 25138334).

Gene information
The IL2RG gene (OMIM: 308380) encodes the common gamma chain, an important subunit of several interleukin receptors, which are central to lymphocyte development and function. Upon ligand binding to the IL2 receptor, the gamma subunit interacts with the JAK3 tyrosine kinase for signal transduction (PMID: 26235889; NCBI. https://www.ncbi.nlm.nih.gov/gene/3561. Accessed August 2017).

Pathogenic variants in the IL2RG gene follow X-linked recessive inheritance. A female with a pathogenic variant has a 50% chance of passing the variant on to her offspring. Males who inherit a pathogenic variant will be affected, and females who inherit a pathogenic variant will be carriers. Males with a pathogenic variant will pass it to all of their daughters, who will be carriers, while none of their sons will inherit the variant. Pathogenic variants may be inherited from a carrier mother or may occur de novo. Germline mosaicism has been reported in mothers of individuals with X-SCID, therefore negative carrier status in the mother does not eliminate the recurrence risk in future pregnancies (PMID: 9049783). With a positive result, it is possible to identify at-risk relatives who can pursue testing for the specific familial variant.

Identification of at-risk, asymptomatic newborns and reconstitution of the immune system with HCT provides a cure for individuals with X-SCID (PMID: 25937517). HCT within the first 3-4 months of life is associated with better outcomes, fewer pre- and post-transplant infections, and faster engraftment compared with cases where HCT is delayed (PMID: 15032591). Outcomes are best when grafts are received from an HLA-matched, related donor; however, transplants from unrelated matched donors and haploidentical donors are also successful (PMID: 25075835). Pre-transplant conditioning regimens vary by donor type and transplant center. Between the time of diagnosis and HCT, individuals with SCID are monitored intensively and treated with immunoglobulin replacement, prophylactic antibiotics, and avoidance of transfusions, immunizations, and exposure to infectious environments. Guidelines for long-term follow-up for individuals with SCID who have undergone HCT have been developed by an international consortium (PMID: 28479164).

Experimental gene therapy for X-SCID is considered for individuals who are not eligible for HCT or for whom the transplant was not successful. With novel methods of gene editing, correcting the gene defects may lead to new treatment options for these individuals (PMID: 28270364). Clinical trials utilizing gene therapy are ongoing.

Review date: August 2017

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below. In addition, the analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
IL2RG NM_000206.2