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Novel compound heterozygous mutations in a Japanese girl with Janus kinase 3 deficiency. Severe combined immunodeficiency (SCID) is the most severe form of primary immunodeficiency disease, and it is characterized by marked impairment in cellular and humoral immunity. Mutations in several genes cause SCID, one of which is Janus kinase 3 (JAK3), resulting in autosomal recessive T(-)B(+)NK(-) SCID. Only three patients with JAK3-deficient SCID have been reported in Japan. We herein describe the case of a 6-month-old girl with pneumocystis pneumonia, who was diagnosed with SCID with compound heterozygous JAK3 mutations (c.1568G>A + c.421-10G>A). One of the mutations was previously reported in another Japanese patient. The other mutation was a novel and de novo relatively deep intronic mutation causing aberrant RNA splicing. The patient was successfully treated with bone marrow transplantation from a haploidentical donor.