We identified a 0.74 Mb deletion from case 1 at chromosome 22q11.2 region, which contains the LZTR1 gene located in the central region of 22q11.2 deletion syndrome (Velocardiofacial/DiGeorge syndrome) manifested as severe congenital heart disease, cleft palate and other specialized facial features, and severe immunodeficiency. Here, LZTR1 is linked to immunodeficiency disease.