We found one pathogenic variant in the NFKB1 gene in a father and his daughter, one pathogenic variant in the TNFRSF13B gene, and one pathogenic variant in the MAGT1 gene associated with X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection, and neoplasia (XMEN syndrome). Here, TNFRSF13B is linked to Epstein-Barr virus infection.