Any mitochondrial complex deficiency in which the cause of the disease is a mutation in the ATP5F1D gene. The disease is mitochondrial complex V (ATP synthase) deficiency, nuclear type 5 (MONDO_0020858, a Monarch Disease Ontology entry). Also known as: MC5DN5, MITOCHONDRIAL COMPLEX V (ATP SYNTHASE) DEFICIENCY, NUCLEAR TYPE 5, Mitochondrial Complex 5 (ATP Synthase) Deficiency, ATP5F1D Type, mitochondrial complex v (atp synthase) deficiency.