An Unexpected Diagnosis of MAGT1 Deficiency in a Patient with CVID-like Features, Molluscum Contagiosum and Atopy

A 6-year-old boy presented to the immunology clinic with recurrent infections. He started to have recurrent otitis media at the age of 18 months. He also had multiple sinus infections and 3–4 episodes of pneumonia. Immunologic evaluation revealed an IgG of 498 (ref 608–1229 mg/dL), an IgA of 20.8 (ref 33–200 mg/dL) and an impaired response to the Streptococcus pneumoniae vaccine. T and B lymphocyte counts were normal. He was started on subcutaneous immunoglobulin replacement therapy after which his IgG level normalized and his frequency of sinopulmonary infections improved. He also has a history of eczema, chronic cough and environmental allergies for which he receives allergen-specific subcutaneous immunotherapy in addition to treatment with an inhaled corticosteroid and omalizumab. The patient also had persistent skin warts on his hands and extensive molluscum contagiosum lesions. He underwent targeted genetic testing for a primary immunodeficiency which revealed a hemizygous pathogenic variant in the magnesium transporter 1 (MAGT1) gene (c.580dup; p.Ser194Phefs*3). This variant is a duplication at nucleotide position 580 that creates a premature stop codon 3 amino acids downstream from this location. The patient subsequently underwent a carbohydrate deficient transferrin test (CDT) for congenital disorders of glycosylation (CDG) that revealed moderately elevated transferrin mono-oligosaccharide to di-oligosaccharide and Apo CIII-1/Apo CIII-2 ratios, consistent with the diagnosis of MAGT1-CDG (XMEN; X-linked immunodeficiency with magnesium defect, EBV infection, and neoplasia). Additionally, NKG2D surface expression was reduced by ~90% on the CD8T cells, and by ~85% on the NK cells in the patient sample compared to the control sample assessed in parallel. The patient continues to test negative for EBV infection by PCR. XMEN disease (OMIM number 300853) is a rare, combined immunodeficiency resulting from a mutation in the magnesium transporter 1 gene (MAGT1) located on the X chromosome. Only 36 patients have been reported to have this disease thus far. While the clinical phenotype is variable, the disease is often associated with EBV infection. This case is unique in that the patient was diagnosed due to a history of severe warts, atopy, and hypogammaglobulinemia in the absence of EBV infection.