Skip to main content

Homozygous R396H mutation of the RAG1gene in a Saudi infant with Omenn's syndrome: a case report



The V(D)J rearrangement of B and T cell lymphocytes during the recombination process, which is essential for the development of normal immune system function, depends critically on the presence of the recombination activating enzymes, RAG1 and RAG2. Mutations in RAG1 or RAG2 can lead to a spectrum of disorders, ranging from typical B-T-severe combined immunodeficiency to Omenn's syndrome.

Case presentation

A two-month-old Saudi baby girl presented with fever, respiratory distress due to bronchiolitis, exfoliative erythroderma and a family history of childhood death within the first few months of life in two of her sisters who had had a similar clinical presentation to her own. Immunological work-up revealed an absence of circulating B lymphocytes, whereas various numbers of activated T lymphocytes were present in the peripheral blood and in the skin.


In this case, mutation analysis of the recombination activating genes RAG1 or RAG2 revealed a homozygous missense (c.1299G>A) mutation in the RAG1 gene. This is the first report in the literature linking a homozygous R396H mutation in the RAG1 gene with presentation of Omenn's syndrome.


Omenn's syndrome (MIM 603554) is an autosomal recessive form of severe combined immunodeficiency (SCID) characterized by early-onset generalized exfoliative erythroderma, desquamation, alopecia, chronic diarrhea, failure to thrive, lymphadenopathy, hepatosplenomegaly and elevated IgE levels. In early infancy, patients with SCID develop potentially life-threatening recurrent infections that may be caused by common bacterial, fungal, or viral infections.

Laboratory findings reveal a characteristic hypereosinophilia and hypogammaglobulinemia. However, IgE serum levels are increased paradoxically in the absence of detectable B lymphocytes in peripheral blood and in skin and lymph node tissues [1, 2].

Both B and T cell lymphocytes undergo the recombination process of V(D)J rearrangement that is essential for the development of normal immune function, and the recombination activating enzymes RAG1 and RAG2 play a crucial role in this recombination [3]. Molecular genetic studies have been focused on elucidating the molecular basis of the B-T- subgroup of SCID that is associated with Omenn's syndrome.

Mutation analysis studies involving SCID and Omenn's syndrome have identified mutations in RAG1 and RAG2[1] that may show differing clinical presentations depending on the type of mutation. When mutations in the recombinase genes RAG-1 and RAG-2 have been explored, homozygous and heterozygous mutations have been found. In contrast to T cell negative (T), B cell negative (B), and natural killer cell positive (NKC+) SCID, in which RAG-1 and RAG-2 mutations affect the active core of the gene, homozygous mutations affecting the active core have not been observed in Omenn's syndrome. Approximately half of the mutations are missense mutations, while the remainder are nonsense, deletion, frameshift, duplication, and splice mutations[1, 4].

Here, we describe a Saudi female infant who was the 8th child of first-degree relative parents (Figure 1). Family history was positive for two early infantile deaths with clinical manifestations consistent with Omenn's syndrome, as shown in this patient. The patient was shown to be a homozygote for mutations in the RAG1 gene.

Figure 1
figure 1

Pedigree of the Saudi family with Omenn's syndrome. Blackened symbol indicate proband. Diagonal lines across symbols indicate deceased individuals.

Case presentation

Our case is that of a two-month-old Saudi female (Figure 1). The family has a history of two early infantile deaths from undiagnosed recurrent chest infections associated with generalized skin erythema. Pregnancy and delivery were uncomplicated. Birth weight was 3500 g. At the age of 2 weeks, the infant presented with generalized scaly erythroderma associated with persistent fever and later developed pneumonia. There was no lymphadenopathy and no hepatosplenomegaly. Subsequently, she developed protracted diarrhea and failure to thrive. The patient had elevated numbers of circulating white blood cells and low hemoglobin (Hb). Flow cytometry showed a critically low (absent) B-cell count with a predominance of T cells (82%) that showed high memory (CD45RO) and activation (CD25) expression. There were normal levels of natural killer cells with normal expression of gamma/delta TCR cells, but no detectable CD19+ or CD20+ B-cells. Both CD4 and CD8 T cells were significantly suppressed; only 21% of CD4 and 33% of CD8 were activated in response to phytohemaglutinine (PHA). Humoral immunity was also abnormal, with elevated serum IgE levels. The nature of the T cells and the remarkable absence of the circulating B cells raised the possibility of a defect in immunoglobulin gene recombination. The histopathological finding of the skin biopsy revealed atypical lymphoid cells that are occasionally noted in the dermal infiltrate. The immunostaining showed that most of the lymphoid cells infiltrating the dermis were of T cell type. The staining of S-100 (polyclonal) was negative in the target cell, suggesting an absence of normal follicles. RAG mutation analysis of our patient revealed a homozygous missense mutation (c.1299G>A) in the RAG1 gene leading to replacement of the normal Arginine (R) amino acid to Histidine (H) at the 396 codon position (R396H) of the resultant normal protein.

This is the first report in the literature showing a homozygous R396H mutation in the RAG1 gene presenting itself with features of Omenn's syndrome. Our patient presented with some of the typical clinical manifestations of Omenn's syndrome that are characterized by a generalized early-onset of exfoliative erythroderma, persistent infection, alopecia, elevated IgE level and elevated white blood count due to lymphocytosis. Skin biopsy showed autologous T-cell infiltration and the absence of a germinal center, which is consistent with histopathological findings in Omenn's syndrome [5].

The patient had no B cells, and the majority of her WBCs were T cells that had a very high expression of the CD45RO memory marker and IL-2R (CD25). Both CD4 and CD8 T cells showed significantly reduced capacity to respond to PHA stimulation. Villa et al. (2001) and Corneo et al. (2001) described patients who showed a nearly complete absence of B cells, reduced number of T cells, and normal NK.

The RAG mutation analysis in our patient revealed a homozygous missense mutation (c.1299G>A) in the RAG1 gene, which led to the replacement of the normal Arginine amino acid to Histidine at the 396 codon position of the resultant normal protein. This mutation has been previously reported in association with Omenn's syndrome in which this missense mutation (c.1299G>A) was detectable in a patient who was heterozygous for the allele; the mutation was associated with a protein-truncating mutation [4, 6].

The location of this missense mutation (i.e., R396H) is within the RAG1 homeodomain region, which is responsible for the recognition of and binding to the nonamer motif of the recombination signal sequence (RSS) [6]. Biochemical analysis performed on classic Omenn's syndrome cases that are harboring a one-allele missense mutation in their RAG1 gene maintained partial V(D)J recombination activity, which accounted for the generation of detectable numbers of activated, anergic, oligoclonal T-lymphocytes [6]. In our case, the lack of circulating B cells, together with oligoclonal expansion of T cells, raised the possibility of RAG deficiency despite the clinical presentation. We suspect that the presence of a homozygous R396H mutation in our patient likely destroyed the function of the RAG1 protein and hence impaired the recombination activity that may be associated directly or indirectly with impairment in B cell immunity. The result of this may be an increased occurrence of life-threatening infections, and, without proper treatment, the condition may lead to death within the first year of life. This explains the death of our patient's two sisters who presented with symptoms consistent with Omenn's syndrome during their few months of life.


This is the first report in the literature showing a homozygous R396H mutation in the RAG1 gene being linked to features of Omenn's syndrome. Consanguineous marriages increase the risk of autosomal recessive disorders. Therefore, choosing to undergo premarital screening, prenatal diagnosis and genetic counseling should be an important consideration for family future planning.


Written informed consent was obtained from the patient for publication of this case report. A copy of the written consent is available for review by the Editor-in-Chief of this journal.



natural killer cell


severe combined immunodeficiency.


  1. Santagata S, Villa A, Sobacchi C, Cortes P, Vezzoni P: The genetic and biochemical basis of Omenn syndrome. Immunol Rev. 2000, 178: 64-74. 10.1034/j.1600-065X.2000.17818.x.

    Article  CAS  PubMed  Google Scholar 

  2. Tabori U, Mark Z, Amariglio N, Etzioni A, Golan H, Biloray B, Toren A, Rechavi G, Dalal I: Detection of RAG mutations and prenatal diagnosis in families presenting with either T-B- severe combined immunodeficiency or Omenn's syndrome. Clin Genet. 2004, 65: 322-326. 10.1111/j.1399-0004.2004.00227.x.

    Article  CAS  PubMed  Google Scholar 

  3. Sobacchi C, Marrella V, Rucci F, Vezzoni P, Villa A: RAG-dependent primary immunodeficiencies. Hum Mutat. 2006, 27: 1174-1184. 10.1002/humu.20408.

    Article  CAS  PubMed  Google Scholar 

  4. Villa A, et al: V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. Blood. 2001, 97: 81-88. 10.1182/blood.V97.1.81.

    Article  CAS  PubMed  Google Scholar 

  5. Martin JV, Willoughby PB, Giusti V, Price G, Cerezo L: The lymph node pathology of Omenn's syndrome. Am J Surg Pathol. 1995, 19: 1082-1087. 10.1097/00000478-199509000-00013.

    Article  CAS  PubMed  Google Scholar 

  6. Villa A, Santagata S, Bozzi F, Giliani S, Frattini A, Imberti L, Gatta LB, Ochs HD, Schwarz K, Notarangelo LD, Vezzoni P, Spanopoulou E: Partial V(D)J recombination activity leads to Omenn syndrome. Cell. 1998, 93: 885-896. 10.1016/S0092-8674(00)81448-8.

    Article  CAS  PubMed  Google Scholar 

Download references


The authors thank King Abdullah International Medical Research Center for their financial support.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Mohammed Al Balwi.

Additional information

Competing interests

The authors declare that they have no competing interests.

Authors' contributions

MB was in charge of designed, a major contributor to the manuscript and overall supervision of the study. SA was involved in the clinical evaluation of the patient while IA carried out the sequencing of the genes and the analysis of the genetic data. AH was performed the immunological evaluation of the patient and a contributor to the manuscript. All authors read and approved the final manuscript.

Rights and permissions

Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution License ( ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Reprints and permissions

About this article

Cite this article

Al Balwi, M., Al Ajaji, S., Al Abdulkareem, I. et al. Homozygous R396H mutation of the RAG1gene in a Saudi infant with Omenn's syndrome: a case report. Cases Journal 2, 8391 (2009).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: