A novel nonsense mutation in MYO15A is associated with non-syndromic hearing loss: a case report

Hearing loss is one of the most prevalent neurosensory defects in the general population. On average, about 1–2 in 1000 newborns have congenital or prelingual deafness [1, 2]. Among the common causes of deafness, approximately 50–60% can be attributed to genetic factors [3]. Hereditary deafness can be classified as being syndromic (about 30%) or non-syndromic (about 70%) [4]. Autosomal recessive inheritance states account for 77–93% of hereditary hearing loss [5]. To date, 105 loci associated with autosomal recessive non-syndromic hearing loss (DFNB) have been mapped and 67 genes have been identified (http://hereditaryhearingloss.org). In particular, GJB2, SLC26A4, MYO15A, OTOF, and CDH23 are the most common genes responsible for hereditary hearing loss [5, 6].

Mutations in MYO15A can lead to DFNB3 (OMIM: 600316). By performing a genome-wide disequilibrium study in 1995, MYO15A was found to be associated with deafness for the first time in Indonesian residents [7, 8]. MY015A encodes an unconventional MYO15A protein, which is a structural constituent of hair cells and stereocilia. Clinically, mutations in MY015A have manifested as profound, congenital, non-syndromic hearing loss [9]. With the extensive application of next generation sequencing, genetic diagnosis is playing a more important role in the prenatal diagnosis and clinical evaluation of MYO15A-associated hereditary hearing loss [10, 11]. However, there are still a large number of variants of undetermined significance, which makes the interpretation of variant effects challenging.

In the present case, we collected and analyzed the clinical genetics data from a family with autosomal recessive non-syndromic hearing loss (ARNSHL). We identified compound heterozygous mutations in MYO15A including a novel nonsense mutation, which induced pathogenic effects on the protein function and therefore should be responsible for the deafness in this family.

Hereditary non-syndromic hearing loss is highly heterogeneous. By the time we provided genetic counseling, the mother of the proband was pregnant. The conventional genetic strategy for screening the causative mutations in this ARNSHL family is time-consuming and impractical. Therefore, we conducted target capture sequencing, which is more suitable for clinical diagnosis with higher sequencing depth and lower costs over whole-exome sequencing.

In this case, we identified compound heterozygous mutations in the MYO15A gene of the proband. These mutations included a novel nonsense mutation, c.6892C > T reported here for the first time and another potentially pathogenic deletion, c.10251_10253delCTT, previously described by Yang et al. [12]. The ASSR audiogram showed severe hearing loss in the proband. Moreover, his ABR and DPOAE tests were negative despite high levels of stimulation, indicating profound deafness, which is consistent with the MYO15A-related prelingual deafness phenotypes.

Myosin belongs to the actin-based motor molecule superfamily and plays an important role in normal auditory function. Unconventional myosins serve in intracellular movements since their highly divergent tails bind to membranous compartments [13]. Mutations in five unconventional myosin genes MYOIA, MYOIIIA, MYOVI, MYOVIIA, and MYOXVA have been reported to cause hearing loss.

MYO15A is located at 17p11.2, which has 66 exons encoding for 3530 amino acids. This protein is expressed at the tips of inner ear sensory cells. The tip is the site of stereocilia growth and is necessary for actin microfilament organization [14]. Shaker-2 mice harboring MYO15A mutations [15], exhibited profound deafness and had much shorter stereocilia than wild-type mice [16]. Thus, the myosin XVa protein is critical for the elongation and differentiation of inner ear hair cells and is required for the arrangement of stereocilia in mature hair bundles [17].The MYO15A protein consists of multiple domains, which include an N-terminal and a motor domain, a neck region and a tail region [18]. Pathogenic mutations, which have no preferential distribution within the MYO15A gene, have been found in all domains [19].

The p.R2298* mutation was observed between the first MyTH4 and FERM domains. The premature termination of translation resulted in the loss of the tail region of the MYO15A protein and the consequential loss of normal protein function. The SH3-MYTH4-FERM tail region domain is also known for its ability to bind to whirlin [20], which is necessary for the elongation and maintenance of hair cell stereocilia in the organ of Corti. Truncated proteins often lead to nonsense-mediated decay and the consequential loss of normal protein function. Several other nonsense mutations of MYO15A gene, including p.W1975∗, p.S2661*, p.R2923*, p.Y2819* and p.Q3264* [19, 21, 22], have been reported to cause hearing loss. The damaged domain caused by p.R2298* mutation is larger than those by many other known pathogenic nonsense variants, leading one to conclude that the nonsense mutation reported here would definitely lead to a pathogenic state. The second mutation p.F3420del was reported previously in an epidemiology study. It is located in the second FERM domain of the MYO15A protein. Previous reports suggested that the MyTH4-FERM domain is required for its localization to stereocilia tips and enriching the adhesion molecules, actin-regulatory proteins [23]. Mutations in this domain could also r result in losing the normal function of the MYO15A protein. In addition, bioinformatics analysis using Mutation Taster and SIFT supported the hypothesis of pathogenicity of both variants. Structural modeling demonstrated that the p.R2298* and p.F3420del variants altered the normal MYO15A protein structure.

Collectively, our study demonstrated that the compound heterozygous c.6892C > T and c.10251_10253delCTT mutations in MYO15A gene were the pathogenic variants in this ARNSHL family. The c.6892C > T nonsense mutation is reported for the first time. Data presented here extend the pathogenic mutation spectrum of the MYO15A gene, which has implications in genetic counseling for hereditary deafness. Functional investigations are needed to further elucidate the pathogenic mechanism of these two mutations.