Any mitochondrial proton-transporting ATP synthase complex deficiency in which the cause of the disease is a mutation in the ATP5F1E gene. The disease is Monarch Disease Ontology entry MONDO_0013547 (mitochondrial complex V (ATP synthase) deficiency, nuclear type 3). Also known as: ATP5F1E mitochondrial proton-transporting ATP synthase complex deficiency, MC5DN3, mitochondrial proton-transporting ATP synthase complex deficiency caused by mutation in ATP5F1E.