Introduction
Hearing loss (HL) is a frequent sensory disorder in humans with an onset at different stages of life. HL occurs in approximately 1:1000 newborns [
1] and the number rises to 3.5:1000 in adolescence [
2]. A genetic mechanism is causative for the disorder in approximately half of children affected by prelingual HL. In the majority of these cases (70%), HL is not accompanied by further symptoms and is, therefore, termed as non-syndromic (NSHL) [
3].
The genetic diagnosis of NSHL remains a challenge in many patients due to the high number of genes involved in the disease. The most common causative gene is
GJB2 in the DFNB1 locus that encodes Connexin 26 (gap junction protein, beta-2), a gap junction protein expressed within the stria vascularis, which regulates cochlear development and is essential for maintenance of active cochlear amplification [
4]. Variations in
GJB2 account for up to 50% of all genetically caused NSHL cases in Caucasians [
5].
Although variations in
GJB2 almost exclusively cause prelingual autosomal recessive HL, the frequency of heterozygous c.35delG in the newborn hearing-impaired population is over 11% compared to a carrier frequency of below 2% in the normal-hearing Austrian population [
6]. Whereas screening within
GJB2 heterozygous patients can also lead to the identification of recessive pathogenic variations in additional HL genes [
7], we originally hypothesized here that novel alterations affecting the cochlear gap junction network within DFNB1 may be the cause for this discrepancy. Thus, the index patient examined in this study, carrying the heterozygous c.262G>T (p.Ala88Ser) recessive
GJB2 transversion [
8], has been prescreened for changes in upstream regulatory sequences [
9], the basal promoter [
10] and alternative transcriptional start sites [
11] and deletions in
GJB6 [
12].
In patients where pathogenic changes in DFNB1 are not found, monosymptomatic HL can be due to genetic defects in any of 90 genes identified to date or alterations in unidentified causative genes [
13]. Whereas variations in most non-DFNB1 genes cause hereditary NSHL only in isolated families, some variations have been shown to have a high prevalence in certain populations. For example, pathogenic variations in the
TMC1 gene (encoding the transmembrane channel-like protein 1) are found in more than a third of hearing-impaired Jewish patients of Moroccan ancestry [
14]. With the exception of variations in
GJB2, no such common genetic variants have been identified to date in the Austrian population. Due to practical and financial considerations, routine genetic HL screening in Austria has therefore been confined to screening the coding sequence of
GJB2, thereby excluding almost 50% of affected individuals from genetic diagnosis and counseling.
Massively parallel DNA sequencing (MPS) allows the comprehensive variation screening of all known deafness genes simultaneously. This high-throughput DNA sequencing method has proven to produce technically reliable results in a time- and cost-efficient manner and is gradually being integrated into the routine genetic diagnostics of Mendelian diseases, including hereditary HL [
14‐
16].
In this study, we applied whole-exome sequencing (WES) on DNA samples from an Austrian family of Turkish origin with monosymptomatic genetic HL containing an index patient bearing a heterozygous c.262G>T pathogenic (p.Ala88Ser) transversion. Extended screening of a hearing-impaired cohort consisting of index patients from 24 families of Turkish origin was subsequently performed to estimate the frequency of the disease-causing variants detected by WES in the Austrian-Turkish HL population.
Discussion
In the index family under study, the normal-hearing father and the affected son, suffering from non-syndromic autosomal recessive HL, were carriers of a known c.262G>T pathogenic variant in the
GJB2 gene (Table
1). No second variation within the
GJB2 gene had been identified in previous genetic screening of the patient. Another possible molecular cause for hearing loss in the index patient could have been a digenic inheritance pattern associated with a second variation in the
GJB6 gene that have been described previously [
14,
22]. However, digenic
GJB2/GJB6 hereditary hearing loss had been excluded in the patient as described previously [
12].
Identification of the homozygous known pathogenic transversion c.5492G>T in Myo15a as the underlying causative variation highlights the importance of involving deaf individuals with heterozygous GJB2 variations in screening for other causative genes. Extending screening for c.5492G>T to a cohort of index patients from 24 families of Turkish descent with congenital HL resulted in a genetic diagnosis in an additional family.
Myosins form a large family of ATP-dependent motor proteins that interact with actin and are essential for a plethora of cellular motility functions. Myosin 15a is a large protein of 3530 amino acids encoded by 66 exons and containing a 1233-residue proline-rich N-terminal domain, an ATPase motor domain, a neck domain with two IQ motifs and a long (1587 amino acids) tail with two myosin tail homology 4 (MyTH4) domains, two band 4.1/ezrin/radixin/moesin (FERM) domains, an Src-homology-3 (SH3) domain and a C-terminal PDZ class I ligand [
23,
24].
Myosin 15a is expressed in cochlear outer and inner hair cells and accumulates in the tips of stereocilia. It has been shown to be essential for delivering compounds to the tips that are required for stereocilia elongation during development and for stereocilia maintenance [
24‐
26]. In mice, a variation in the motor domain of Myosin 15a causes the deaf-circling shaker 2 (sh2) phenotype [
27] and in humans, variations in
Myo15a are the cause for DFNB3 type deafness [
28]. All known pathogenic variations in
Myo15a cause prelingual HL [
29].
The missense transversion in exon 22 at c.5492G>T (p.Gly1831Val) replaces a highly conserved glycine residue in the Myosin 15a motor domain with valine. Molecular modeling has previously predicted that p.Gly1831Val may inhibit the ability of Myosin 15a to perform the power stroke, which is essential for myosin movement along actin filaments [
21].
The
Myo15a c.5492G>T variant identified is a very rare missense variation so far only identified in a single family with congenital HL in Turkey [
21] and is not listed in over 277,000 alleles in the gnomAD database. Our results confirm the pathogenicity of this variant. All three individuals with the homozygous c.5492G>T variation identified in this study and the family described previously show a similar phenotype with profound congenital HL, indicating that this variation has a high penetrance. Families TAR1 and TAR6 had no obvious blood-relationship and none of the family members recalled any positive family history of ancestors that suffered from HL. The occurrence of a homozygous single nucleotide change in three unrelated families can be explained by traditional consanguineous mating in the present population and is most likely the result of a founder allele from a common ancestor. Since the c.5492G>T variation was not present in any of the other 23 families tested in this study, it is likely to play a minor role in the pathogenesis of HL in the general Turkish population.
WES allowed a rapid and cost-effective diagnosis in family TAR1. Traditional homozygosity mapping and candidate gene sequencing would have been a very laborious and costly approach due to the large size of the Myo15a gene encoded by 66 exons and would have been of uncertain success due to the small number of available individuals in the index family. The strength of WES in comprehensive screening of large genes and rapid diagnosis even in small families is, therefore, underlined by our results.
Compliance with ethical standards