Patients with influenza-associated encephalopathy exhibit thermal instability of compound variants for [1055T>G/F352C] and [1102G>A/V368I] of carnitine palmitoyltransferase II (CPT II), resulting in secondary CPT II deficiency and mitochondrial energy crisis through disorders of long-chain fatty acid metabolism during hyperpyrexia. Here, CPT2 is linked to Encephalopathy.