Compound Heterozygosity for <i>OTOA</i> Truncating Variant and Genomic Rearrangement Cause Autosomal Recessive Sensorineural Hearing Loss in an Italian Family

Hearing loss (HL) affects 1–3 newborns per 1000 and, in industrialized countries, recognizes a genetic etiology in more than 80% of the congenital cases. Excluding <i>GJB2</i> and <i>GJB6</i>, <i>OTOA</i> is one of the leading genes associated with autosomal recessive non-syndromic HL. Allelic heterogeneity linked to <i>OTOA</i> also includes genomic rearrangements facilitated by non-allelic homologous recombination with the neighboring <i>OTOAP1</i> pseudogene. We present a couple of Italian siblings affected by moderate to severe sensorineural hearing loss (SNHL) due to compound heterozygosity at the <i>OTOA</i> locus. Multigene panel next-generation sequencing identified the c.2223G>A, p.(Trp741*) variant transmitted from the unaffected mother. Assuming the existence of a second paternal deleterious variant which evaded detection at sequencing, genomic array analysis found a ~150 Kb microdeletion of paternal origin and spanning part of <i>OTOA</i>. Both deleterious alleles were identified for the first time. This study demonstrates the utility of an integrated approach to solve complex cases and allow appropriate management to affected individuals and at-risk relatives.