Epilepsy with auditory features: A heterogeneous clinico-molecular disease

Abstract

Objective: To identify novel genes implicated in epilepsy with auditory features (EAF) in phenotypically heterogeneous families with unknown molecular basis.

Methods: We identified 15 probands with EAF in whom an LGI1 mutation had been excluded. We performed electroclinical phenotyping on all probands and available affected relatives. We used whole-exome sequencing (WES) in 20 individuals with EAF (including all the probands and 5 relatives) to identify single nucleotide variants, small insertions/deletions, and copy number variants.

Results: WES revealed likely pathogenic variants in genes that had not been previously associated with EAF: a CNTNAP2 intragenic deletion, 2 truncating mutations of DEPDC5, and a missense SCN1A change.

Conclusions: EAF is a clinically and molecularly heterogeneous disease. The association of EAF with CNTNAP2, DEPDC5, and SCN1A mutations widens the phenotypic spectrum related to these genes. CNTNAP2 encodes CASPR2, a member of the voltage-gated potassium channel complex in which LGI1 plays a role. The finding of a CNTNAP2 deletion emphasizes the importance of this complex in EAF and shows biological convergence.

Figure 1. Segregation and localization of the identified variants

Pedigrees of the mutated families with mutations and schematic representation of the genes and the identified variants are presented. Phenotype labels: EAF = epilepsy with auditory features; GTCS = generalized tonic-clonic seizures; GS = generalized seizures; FS = febrile seizures; unclassified: it is undetermined whether the seizure type is focal or generalized. Gene diagrams and variants: blue lines represent the genomic regions spanned by the gene, while the blue bars represent the exons. Colored blocks surrounding gene regions correspond to the protein domains encoded by the embedded exons. DEP = Dishevelled, Egl-10 and Pleckstrin domain; D1-4 = domains 1–4; F5/8 = discoidin domain; LGL = laminin G-like domain; EL = EGF-like domain; FCT = fibrinogen C-terminal domain; TM = transmembrane domain. The probands' Sanger sequencing electropherogram surrounding the variant site is reported. The histogram plot represents the result of the real-time PCR. Log2ratios of ΔΔCt from patient A:III:1, patient A:IV:1, and a normal individual each against a control sample are plotted. The control sample is one that was negative for CNTNAP2 rearrangements by array comparative genomic hybridization analyses. Four probes were tested. Probe 1 and probe 2 are located in intron 1, while probe 3 and probe 4 are located in intron 3.

Figure 2. The CNTNAP2 locus in disease and localization of its encoded product, CASPR2, at the synapse

(A) Schematic indicating the functional relationship linking LGI1 and CASPR2 proteins through the voltage-gated potassium channel (VGKC). (B) Schematic indicating the previously reported microdeletions (horizontal bars) of CNTNAP2 in neuropsychiatric conditions (modified from Rodenas-Cuadrado, 2013). The deletion reported in this study, spanning CNTNAP2 exons 2-3, overlaps most of the CNTNAP2 deletions implicated in disorder before. It is represented in red with a halo surrounding it. ADHD = attention-deficit/hyperactivity disorder; ASD = autism spectrum disorder.