Relatively decreased expressions of RT-PCR-amplified FOXP3 and/or RORγt were noted in the “predominantly antibody deficiencies” (Btk, CVID and TTC37), “combined T and B immunodeficiencies” (SCID and CID), “congenital phagocyte disorders” (CGD), “combined immunodeficiencies with associated or syndromic features” (Wiskott-Aldrich syndrome), and “disease of immune dysregulation” (XIAP) categories, and in the “unclassified” category encompassing patients with alopecia, albinism, severe atopic dermatitis or non-tuberculosis infections. Here, FOXP3 is linked to chronic granulomatous disease.