SUMMARY Epileptic encephalopathies are a heterogeneous group of severe seizure disorders accounting for approximately 25% of childhood epilepsies. Mutations in the neuronal citrate transporter SLC13A5/NaCT gene abolish its functional activity, causing early onset epileptic encephalopathy (EOEE). The patients display seizures in the first hours of life, and experience developmental delays. The Na+-driven citrate transporter (NaCT) is located in the plasma membrane of neurons. As an intermediate of the citric acid cycle, citrate is critical for energy production in the cell, and it acts as a precursor for the synthesis of lipids and neurotransmitters. Disruption of this citrate import process is therefore understandably harmful to neurons. According to their cellular expression patterns, mutations causing EOEE have been classified as two types. Whereas Type I (protein located in the ER) reduces protein stability, Type II (protein located in the plasma membrane) directly affects the substrate and sodium binding sites or blocks the conformational changes necessary for transport. Based on a homology model of NaCT built from our crystal structure of the bacterial succinate transporter VcINDY, we postulate how each type of mutation alters the NaCT structure and hinders transport activity. We will characterize the mechanisms and structural changes using a combination of biochemical, biophysical and structural approaches. The results will aid in the design of small molecule potentiators and folding correctors with the potential to help the young patients.