Targeted next-generation sequencing revealed a new mutation in GLRA1 gene in a family with Hereditary Hyperekplexia

Introduction Hereditary Hyperekplexia (HPX) is a genetic neurodevelopmental disorder recently defined by the triad of neonatal hypertonia, excessive startle reflexes, and generalized stiffness following the startle. Defects in GLRA1 are the most common cause of HPX, inherited both in an autosomal dominant and autosomal recessive manner. To date, the pathogenetic mechanism of the disease is still not fully understood and a clear genotype-phenotype correlation has not emerged yet. Here we report a new family of patients with a typical HPX phenotype, linked to a novel GLRA1 mutation, inherited with a recessive pattern. OBJECTIVE The aim of this study was to assess the genetic background of a familial case of two siblings affected by HPX, using a targeted Next Generation Sequencing (NGS) panel comprising known HPX-causative genes. MATERIALS AND METHODS After DNA extraction by standard methods and quantization using the Qubit instrument (ThermoFisher Scientific, high coverage targeted NGS data were generated by an amplicon-based approach at the NGS-Core of IRIB-CNR, Mangone. We used a custom-made panel comprising HPX-related genes (GRLA1, GLRB, SLC6A5, GPHN and ARHGEF9). The enriched libraries were sequenced on the Ion Torrent Personal Genome Machine (PGM) system from ThermoFisher Scientific. The alignment and the variant caller was carried out using Ion Torrent Suite 5.10. Annotation and filtering/priorization of single-nucleotide variations (SNVs) and copy number variations (CNVs) discovered was made by Annovar. RESULTS In the present study, the genetic investigation of a familial case of HPX using an amplicon based NGS approach revealed a novel homozygous nonsense variant c.G1509T (p.E403X) in the exon 9 of GLRA1 in both sibling, validated by direct sequencing. No mutations were found in other genes known to cause familial hyperekplexia. The parents, who were first cousins of Pakistani origin, were heterozygous for the p.E403X mutation. The p.E403X variation is a G-to-T substitution at the nucleotide position 1509 in exon 9, replacing glutamate to a premature stop codon at codon 403. DISCUSSIONS We described the case of two siblings with HPX and a novel nonsense mutation c.G1509T (p.E403X) in GLRA1. Localized precisely in loop 3, between the TM3 and TM4 transmembrane domains, the variant causes the deletion of a protein portion, resulting in a truncated protein causing a loss of function, although the delineation of its mechanism requires further investigation. CONCLUSION In conclusion, NGS genetic testing of glycinergic neurotransmission-associated genes including GLRA1, is a readily available tool to confirm clinical suspicion, provide an appropriate diagnosis of HPX and for family screening.