Novel Homozygous Mutation in the MYO15A Gene in Autosomal Recessive Hearing Loss

1. Introduction

Hearing loss is one of the most common sensory disorders that can significantly affected quality of life [1]. Syndromic and non-syndromic hearing loss display in autosomal dominant, autosomal recessive, Y-linked, X-linked or mitochondrial pattern of inheritance [2]. Autosomal recessive nonsyndromic hearing loss (ARNSHL) accounts for up to 80% of cases of NSHL [3]. To date, 61 genes and more than 100 genetic loci have been identified in ARNSHL (http://hereditaryhearingloss.org/).

The most frequently genes involved in ARNSHL are those encoding myosin XVA (MYO15A, MIM# 602666), gap junction protein beta 2 (GJB2, MIM# 121011), solute carrier family 26 (anion exchanger) member 4 (SLC26A4, MIM# 605646), transmembrane channel- like 1 (TMC1, MIM# 606706), otoferlin (OTOF, MIM# 603681) and cadherin-related 23 (CDH23, MIM#605516), each of which has been contained more than 20 various mutations that most of them have been detected in consanguineous families [4]. In present study, we report a case of novel mutation discovered from the direct mutation screening of all exons in the MYO15A gene in an Iranian patient with hearing loss disorder (HLD).

2. Case Presentation

The patient was a 24-years-old male, the only-child of Iranian consanguineous couple (Figure 1A). He was diagnosed with congenital hearing loss and had no dysmorphic features. There was no significant history of hearing loss in this family and no history of systemic disease in the patient.

A, Pedigree of the family; B, The result of genetic sequencing, showing the homozygous missense mutation CTG > CGG in exon 59 of the patient’s MYO15A gene

Figure 1.

A, Pedigree of the family; B, The result of genetic sequencing, showing the homozygous missense mutation CTG > CGG in exon 59 of the patient’s MYO15A gene

2.1. Molecular Analysis

Genomic DNA was extracted from peripheral leukocytes of the patient by the standard salting out protocol, and the PCR was conducted under the following conditions: 200 μM deoxyribonucleotide triphosphates (dNTPs), 100 ng genomic DNA, 2.5 units supertaq polymerase, 1.5 mm MgCl, and 25 pmoL each primer (Table 1). Amplification Carried out in 25 μL volumes and 35 cycles: 94°C for 1 minute, 64°C for 35 seconds and 72°C for 45 seconds. Direct sequencing of the 66 exons performed by using the big dye terminator cycle sequencing ready reaction kit on an ABI Prism 3700 automated genetic analyzer. Finally, the sequencing reactions were carried out and the sequences were compared to the reported gene sequence using the BLASTN program.

The effect of Candidate variant in protein structure and phylogenetic conservation was predicted by using bioinformatic tools like PolyPhen-2 (PolymorphismPhenotyping v2).

3. Results

Sequencing analysis of the patient, after comparison with MYO15A reference sequence in 1000 Genomes database, demonstrated a novel mutation, a homozygous missense mutation, c.9698T > G in exon 59 of the MYO15A gene (Figure 1B). The c.9698T > G mutation is novel and has not been previously described in HLD.

The novel homozygous missense mutation was predicted to be possibly damaging by in silico prediction of the recognized variant, Polyphen 2 (probably damaging, score 1.00).

4. Discussion

We analyzed an affected person with HLD with PCR and direct sequencing of coding exons of the MYO15A gene. As a result we identified a genetic variant of MYO15A in ARNSHL patient. The mutation identified in our patient involved a novel homozygous mutation, c.9698T > G in exon 59, which results in substituting a Leusin to an Arginin (p.L3233A) in the ferm domain and tail region of the Myosin protein. So, this exchange amino acid results in alter a nonpolar amino acid to polar positively charged that can modify interaction of tail region of myosin with membranous compartments and change its movement to actin filaments. This change is predicted to negatively affect the usual function of the myosin XVa protein by in silico. Overall, it seems that this amino acid has an important role in the myosin-XV protein, and mutation at this site results in pathogenicity and deafness.

MYO15A has 66 exons and its coding protein, myosin XVa, has a critical role in formation of stereocilia in hair cells of the cochlea [5]. Myosin XVa in the organ of Corti is localized completely at the tips of stereocilia and is anactin-activated ATPase that uses the hydrolysis of ATP to move on actin filaments. The tip of a stereocilium is one of the proposed sites of mechano-electrical transduction and the site of stereocilia growth [6]. Myosin XVa is required for proper function and formation of the mechanotransduction machinery. All myosins are composed of one or two heavy chains and several light chain. The tails of the myosins presumed to bind to membranous compartments, which would be moved relative to actin filaments [7].

Twenty-nine mutations have been described in MYO15A in HGMD (http:// www.hgmd.org).

In summary, this is the first case with hearing loss in south-west of Iran confirmed by genetic analysis involving a novel MYO15A gene mutation. Further studies are required to understand the structural and functional changes of proteins involved in this disorder and their relations with phenotypic spectrum. Genotype-phenotype relations of MYO15A mutations and degree of hearing loss suggest that mutations in all 66 exons cause intense deafness.