Multiple congenital anomalies-hypotonia-seizures syndrome-2 is a genetic disorder also known as infantile epileptic encephalopathy. This disorder is associated with a mutation in the PIGA gene, resulting in defective in glycosylphosphatidylinositol biosynthesis. Multiple congenital anomalieshypotonia-seizures syndrome has variable clinical symptoms; the severity of the congenital anomalies has been reported to be correlated with the loss of PIGA activity. We report a neonatal case of multiple congenital anomalies-hypotonia-seizures syndrome-2 with a PIGA c.1234C>T (p.Arg412*) mutation, which was discovered by exome sequencing and confirmed by Sanger sequencing. The reported patient had omphalocele, facial dysmorphism, neonatal hypotonia, and seizures. To our knowledge, this is the first report in Korea of a neonatal case diagnosed with multiple congenital anomalies-hypotonia-seizures syndrome-2 associated with a germline PIGA c.1234C>T (p.Arg412*) mutation.