Severe Combined Immunodeficiency/Omenn Syndrome via the RAG1 Gene

Severe combined immunodeficiency (SCID) encompasses a diverse group of rare, life-threatening disorders. While the true incidence of SCID is unknown, newborn screening studies suggest that 1 in 70,000 births are affected with a range of 1 in 40,000 to 100,000 (Fischer. 2000. PubMed ID: 11091267; Kwan et al. 2014. PubMed ID: 25138334; Kumrah et al. 2020. PubMed ID: 32181275). SCID is caused by genetic defects that inhibit lymphocyte development and function, resulting in no T cell differentiation and abnormal development of B and natural killer (NK) lymphocytes (Fischer. 2000. PubMed ID: 11091267; Kumrah et al. 2020. PubMed ID: 32181275). The clinical features associated with SCID include recurrent and severe bacterial, viral, and fungal infections that begin in infancy (Fischer. 2000. PubMed ID: 11091267; Kwan et al. 2014. PubMed ID: 25138334; Kumrah et al. 2020. PubMed ID: 32181275). To date, there are over 20 genes known to be associated with SCID (Allenspach et al. 1993. PubMed ID: 20301584; Bousfiha et al. 2018. PubMed ID: 29226301; Picard et al. 2018. PubMed ID: 29226302; Kumrah et al. 2020. PubMed ID: 32181275; Tangye et al. 2020. PubMed ID: 31953710). The majority of the genes are involved in autosomal recessive SCID; however IL2RG is associated with an X-linked form of the disease (Allenspach et al. 1993. PubMed ID: 20301584).

Patients with SCID due to pathogenic variants in the RAG1 gene lack T and B cells while retaining normal NK cell levels (T-B-NK+ SCID; Bousfiha et al. 2018. PubMed ID: 29226301). Previous studies have shown that RAG1 variants are causative for 5-15% of all cases of SCID (Lindegren et al. 2004. PubMed ID: 14724556; Sarzotti-Kelsoe et al. 2009. PubMed ID: 19433858; Chan et al. 2011. PubMed ID: 21035402; Kwan et al. 2014. PubMed ID: 25138334).

Classification of SCID may be subdivided based on B cell status and further subdivided based on NK cell status (Allenspach et al. 1993. PubMed ID: 20301584; Kumrah et al. 2020. PubMed ID: 32181275). Omenn Syndrome (OS), also known as leaky SCID, typically presents during the first year of life and is characterized by erythroderma, desquamation, eosinophilia, failure to thrive, lymphadenopathy and chronic diarrhea (Ege et al. 2005. PubMed ID: 15731174). Patients with OS have limited B cells and elevated T cell levels with impaired function resulting in a distinct inflammatory phenotype (T+B-NK+ SCID). OS is due to hypomorphic variants predominantly in the RAG1 and RAG2 genes, but DCLRE1C and IL7R can also have causative variants (Villa et al. 2002. PubMed ID: 11908269; Ege et al. 2005. PubMed ID: 15731174; Zago et al. 2014. PubMed ID: 24759676).

Regardless of the type of SCID, it is necessary to establish a genetic diagnosis for genetic counseling, prognostication, and optimization of treatment (Kwan et al. 2014. PubMed ID: 25138334; Kumrah et al. 2020. PubMed ID: 32181275). The recurrence risk and prognosis may vary depending on the underlying genetic cause of the deficiency. In general, the prognosis is poor if there is a delay in diagnosis and therapy. Early hematopoietic stem cell transplantation (HSCT) is the most established treatment for patients with SCID (Kwan et al. 2014. PubMed ID: 25138334).

To date, there are over 20 genes causative for autosomal recessive forms of SCID, including RAG1 (Allenspach et al. 1993. PubMed ID: 20301584; Bousfiha et al. 2018. PubMed ID: 29226301; Picard et al. 2018. PubMed ID: 29226302; Kumrah et al. 2020. PubMed ID: 32181275; Tangye et al. 2020. PubMed ID: 31953710). Variants in IL2RG are causative for X-linked SCID. Variants in IL2RG, ADA, and IL7R account for ~75% of all cases of SCID (Allenspach et al. 1993. PubMed ID: 20301584; Fischer. 2000. PubMed ID: 11091267; Chan et al. 2011. PubMed ID: 21035402). Pathogenic variants in RAG1 account for 5-15% of all cases of SICD (Allenspach et al. 1993. PubMed ID: 20301584; Kalman et al. 2004. PubMed ID: 14726805; Lindegren et al. 2004. PubMed ID: 14724556; Sarzotti-Kelsoe et al. 2009. PubMed ID: 19433858; Chan et al. 2011. PubMed ID: 21035402; Kwan et al. 2014. PubMed ID: 25138334). OS is also inherited in an autosomal recessive manner through variants in the RAG1, RAG2, DCLRE1C, or IL7R genes (Villa et al. 2002. PubMed ID: 11908269; Ege et al. 2005. PubMed ID: 15731174; Zago et al. 2014. PubMed ID: 24759676).

Causative variants in SCID genes may be inherited from unaffected parents or may occur de novo in the patient. Studies analyzing newborns with SCID determined that only ~20% had a family history of immunodeficiency, while ~80% of cases lacked a positive family history (Chan and Puck. 2005. PubMed ID: 15696101; Puck. 2007. PubMed ID: 17931561; Chan et al. 2011. PubMed ID: 21035402; Kwan et al. 2014. PubMed ID: 25138334). Those with a lack of family history are a result of de novo variants and unknown carrier status. These studies analyzed SCID as a whole and did not break down the analysis into the different subtypes of SCID.

Pathogenic variants in RAG1 may lead to a wide range of clinical features, including classic SCID with autoimmunity, hyper IgM syndrome, common variable immune deficiency, and Omenn syndrome or leaky SCID (Kumrah et al. 2020. PubMed ID: 32181275). Patients with more severe clinical features of SCID primarily have null variants in RAG1, while those with OS tend to have hypomorphic variants in RAG1, typically missense, which lead to an impaired but not complete loss of protein function (Villa et al. 2002. PubMed ID: 11908269; Ege et al. 2005. PubMed ID: 15731174). RAG1 variants occur throughout the coding region and are rarely overlapping for SCID and OS (Villa et al. 2002. PubMed ID: 11908269). Overall, most causative variants in RAG1 are missense; however nonsense and small frameshift deletions and insertions have also been reported (Kalman et al. 2004. PubMed ID: 14726805). Gross deletions of the RAG1 gene have been reported in very rare cases (Schwarz et al. 1996. PubMed ID: 8810255; Kato et al. 2015. PubMed ID: 25739914).

The RAG1 gene encodes a DNA recombinase that works to initiate VDJ recombination to create variable immunoglobulin and T cell receptor rearrangements, which are required for B and T cell precursor survival (Kumrah et al. 2020. PubMed ID: 32181275). A deficiency, either complete or partial, of the RAG1 protein will alter VDJ recombination, which would promote the T cells to undergo apoptosis and result in the various forms of SCID (Kumrah et al. 2020. PubMed ID: 32181275).

Mouse models have been utilized to study the pathogenicity of variants in the RAG1 gene. Mouse models with homozygous deletions in Rag1 were found to not have any mature B or T lymphocytes due to an inability to initiate lymphocyte differentiation at an immature stage (Mombaerts et al. 1992. PubMed ID: 1547488). Overall, the loss of RAG1 function led to a SCID phenotype in the mice due to a similar mechanism as is seen in individuals with SCID. A similar phenotype has also been described for Rag2 deficient mouse models (Shinkai et al. 1992. PubMed ID: 1547487). Knockin mouse models have been created in which the endogenous Rag1 was replaced with Rag1 carrying hypomorphic variants. These models had impaired lymphocyte development and decreased VDJ rearrangement and mimicked most of the symptoms of human Omen syndrome (Khiong et al. 2007. PubMed ID: 17476359; Giblin et al. 2009. PubMed ID: 19126872).

Pathogenic variants in RAG1 have been identified in 5-15% of patients presenting with various types of SCID (Lindegren et al. 2004. PubMed ID: 14724556; Sarzotti-Kelsoe et al. 2009. PubMed ID: 19433858; Chan et al. 2011. PubMed ID: 21035402; Kwan et al. 2014. PubMed ID: 25138334). For patients with a known T-B-NK+ immunophenotype or clinical features of OS, clinical sensitivity is improved.

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This test provides full coverage of all coding exons of the RAG1 gene plus 10 bases flanking noncoding DNA in all available transcripts in addition to non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as ≥20X NGS reads or Sanger sequencing.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels.