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GATA6 syndrome is a rare monogenic disorder caused by heterozygous variants in the gene GATA6, which controls the early embryonic differentiation of germ layers and the development of different organs. We present the results of the 7-year follow-up of a child with this syndrome as well as the following conditions: diabetes mellitus, exocrine pancreatic insufficiency, gallbladder atresia, and congenital heart disease (CHD). At birth, the patient was diagnosed with neonatal diabetes mellitus (NDM) associated with heart (mitral valve prolapse) and gastrointestinal abnormalities (gallbladder atresia). Diabetes remitted within weeks and relapsed at the age of 2. We identified a de novo variant of a 4-nucleotide deletion (c.1302+4_1302+7del), previously unreported in the literature, in the donor splicing site of exon 3 of the GATA6 gene in a heterozygous state. Screening for other possible components of GATA6 syndrome revealed exocrine pancreatic insufficiency, and pancreatic enzyme replacement therapy resulted in improved dyspeptic symptoms, and growth rates increased. In addition, the patient was diagnosed with autoimmune thyroiditis and progressive myopia. [ABSTRACT FROM AUTHOR]