EpiSignature Utility for Variant of Uncertain Significance Reclassification in an Apparently Atypical Presentation of...

Current guidelines recommend broad sequencing as a first-tier test for epilepsy, identifying a genetic etiology in 40% of cases. Sequencing subsequently increases the number of patients identified with variants of uncertain significance (VUSs). Clinicians desire additional investigatory methods to better classify these VUSs.

The HNRNPU gene (MIM #602869) is associated with a neurodevelopmental condition characterized by intellectual disability and developmental delay, epilepsy, and characteristic facial features. To date, only de novo variants with complete penetrance have been described. We present a 7-year-old female with HNRNPU variant c.669_691dup; p.Gly231Valfs*116, classified as both pathogenic (Laboratory A) and as a VUS (Laboratory B). This patient exhibits an isolated seizure phenotype, and familial studies revealed the proband's father (asymptomatic), paternal uncle (epilepsy), and paternal grandmother (asymptomatic) all carry this variant. Laboratory B theorized the potential for alternative splicing, reducing concerns about pathogenicity. Methylation studies were pursued for more accurate classification and are conclusively negative for the HNRNPU episignature. This, in the context of the variant not segregating with the familial epilepsy phenotype, indicates a benign classification for the c.669_691dup; p.Gly231Valfs*116 variant.

The number of epilepsy patients with nondiagnostic genetic results requires additional modes of investigation. Reclassification often takes years due to the novelty of variants identified. This case highlights the importance of laboratory scrutiny when multiple variants are detected, the need for greater data sharing between laboratories to reduce inconsistent classifications, and the utility of ancillary testing, such as methylation studies, to aid in VUS reclassification.