Neurological disorders, including seizures, migraine, depression, and intellectual disability, are frequently associated with hypomagnesemia. Specifically, magnesium (Mg2+) channel transient receptor potential melastatin (TRPM) 6 and TRPM7 are essential for brain function and development. Both channels are also localized in renal and intestinal epithelia and are crucial for Mg2+(re)absorption. Cyclin M2 (CNNM2) is located on the basolateral side of the distal convoluted tubule. In addition, it plays a role in the maintenance of plasma Mg2+ levels along with TRPM6, which is present at the apical level. The CNNM2 gene is crucial for renal magnesium handling, brain development, and neurological functioning. Here, we identified a novel mutation in the CNNM2 gene causing a cognitive delay in a girl with hypomagnesemia. We suggest testing for CNNM2 mutation in patients with neurological impairment and hypomagnesemia.