Phosphoglycerate kinase (PGK) deficiency affects three different organs: red blood cells (RBC), the central nervous system, and muscles. Next-generation sequencing identified a hemizygous PGK1 mutation (p. V217I) in a 16-year-old Japanese male patient presenting with intellectual disability and episodes of muscle weakness of unknown etiology. Enzymatic analysis demonstrated slightly lower RBC-PGK activity and compensatory increases of other glycolysis enzymes. This is the first PGK1 mutation found through next-generation sequencing.