RBFOX1 and RBFOX3 mutations in rolandic epilepsy

Abstract

Partial deletions of the gene encoding the neuronal splicing regulator RBFOX1 have been reported in a range of neurodevelopmental diseases, including idiopathic generalized epilepsy. The RBFOX1 protein and its homologues (RBFOX2 and RBFOX3) regulate alternative splicing of many neuronal transcripts involved in the homeostatic control of neuronal excitability. In this study, we explored if structural microdeletions and exonic sequence variations in RBFOX1, RBFOX2, RBFOX3 confer susceptibility to rolandic epilepsy (RE), a common idiopathic focal childhood epilepsy. By high-density SNP array screening of 289 unrelated RE patients, we identified two hemizygous deletions, a 365 kb deletion affecting two untranslated 5'-terminal exons of RBFOX1 and a 43 kb deletion spanning exon 3 of RBFOX3. Exome sequencing of 242 RE patients revealed two novel probably deleterious variants in RBFOX1, a frameshift mutation (p.A233Vfs*74) and a hexanucleotide deletion (p.A299_A300del), and a novel nonsense mutation in RBFOX3 (p.Y287*). Although the three variants were inherited from unaffected parents, they were present in all family members exhibiting the RE trait clinically or electroencephalographically with only one exception. In contrast, no deleterious mutations of RBFOX1 and RBFOX3 were found in the exomes of 6503 non-RE subjects deposited in the Exome Variant Server database. The observed RBFOX3 exon 3 deletion and nonsense mutation suggest that RBFOX3 represents a novel risk factor for RE, indicating that exon deletions and truncating mutations of RBFOX1 and RBFOX3 contribute to the genetic variance of partial and generalized idiopathic epilepsy syndromes.

Figure 1. Overview of RBFOX1 and RBFOX3 affecting variants.

Hg19 genomic localization and overview of known transcript variants. Red bars represent microdeletion size and location for the patient. Red dashes indicate the genomic location of single nucleotide variants. (A) Overview RBFOX1 (B) RBFOX3.

Figure 2. Segregation of RBFOX1 and RBFOX3 affecting variants.

For three mutations for which DNA samples of family members were available, segregation analyses could be performed. The respective RBFOX1 and RBFOX3 truncating mutations co-segregated with a variable phenotype of either seizures or pathologic EEG patterns in most family members. Only a few individuals carried the respective familial mutation but did not present any clinical features, indicating incomplete penetrance of the mutations. However, subclinical phenotypes (e.g. EEG patterns) have not been investigated in these individuals (indicated by question mark). In family 3 the variant (deletion of two consecutive alanine residues at position 299–300 of RBFOX1) did not segregate with the epilepsy phenotype. Abbreviations: n.a = DNA was not available for testing; RE = rolandic epilepsy; CTS = centrotemporal spikes; ESES = encephalopathy with status epilepticus during sleep.