We sought to determine the etiology of RANBP2-negative pediatric patients presenting with acute necrotizing encephalopathy of childhood (ANEC).

ANEC is a rare childhood syndrome associated with fulminant encephalopathy and characteristic neuroimaging typically precipitated by acute infection and often associated with heterozygous mutation in RANBP2. Additional genes implicated in ANEC include CPT2, MC1DN1 and ILAE4, yet many patients who meet clinical criteria for ANEC do not have mutations in any known genes and the cause of these cases has remained cryptic.

We performed a multicenter trio-based whole exome analysis of 12 RANBP2-negative pediatric patients diagnosed with ANEC using our established pipeline and filtering criteria. Whole exome sequencing was performed using a TruSeq exome capture kit and run on an Illumina NovaSeq 6000. Fastq files were analyzed using our established GATK-based pipeline and filtered for rare variants using our published approach. We prioritized rare candidate genes to determine plausible candidates based on the existing literature.

32 candidate genes survived filtering and were considered in our analysis. We identified three high-confidence candidate genes. The first was SCN1A, segregating a heterozygous de novo (p.F1765Cfs*28). SCN1A encodes a voltage-gated sodium channel subunit. Mutations in SCN1A are well-known causes of Dravet Syndrome and other forms of epilepsy, but have also been associated with a fulminant encephalopathy phenotype independent of seizure burden. The second was TNFAIP3 (heterozygous de novo p.R728C), previously shown to lead to an autoinflammatory Behcet-like syndrome. The third was PRF1 (homozygous p.R225W), associated with a hemophagocytic lymphocystiocytosis-like phenotype with encephalopathy, ataxia, deep white matter lesions, and increased intracranial pressure.

Our study indicates that ANEC is genetically heterogeneous and highlights three additional genes that should be considered in individuals presenting with ANEC. Our results also showcase how monogenic conditions can impact immune system regulation and lead to neuroimmunologic disorders.