Isa Abdi Rad
Urmia University of Medical Sciences, Iran
Title: Spectrum of MYO15A mutations and report of a Novel Splicing Mutation in an Iranian Family with Sensorineural Hearing Loss
Biography
Biography: Isa Abdi Rad
Abstract
Autosomal recessive non-syndromic hearing loss is a genetically heterogeneous defect which affects millions of people in the world. In this study‚ we performed clinical exome sequencing in a patient with a non-syndromic sensorineural hearing loss and found a novel mutation (c.9611_9612+8del) in MYO15A gene which creates a shift in the reading frame starting at codon 3204. The new reading frame ends in a stop codon 16 positions downstream. This variant has been confirmed by Sanger sequencing and the family analysis showed the mutation segregates with hearing loss.
To the best of our knowledge, this mutation has not been reported in any data base.
Introduction
Non-syndromic sensorineural hearing loss (SNHL) is the most common sensorineural disorder accounts for ~70% of hereditary hearing loss which 80% of cases have an autosomal recessive mode of inheritance (ARNSHL)[1].To date, Over 60 genes and more than 100 genetic loci have been identified for ARNSHL (Hereditary Hearing Loss Homepage, http:// hereditaryhearingloss.org). The genes GJB2, SLC26A4, MYO15A, OTOF, and CDH23 are most commonly implicated in ARNSHL[2].
MYO15A Mutations (NM_016239) have been reported to cause sensorineural hearing loss in human [autosomal recessive 3 (DFNB3)][3]. The DFNB3 locus (OMIM-600316) was first identified in an isolated village in Indonesia where 2% of their population had affected by hearing loss Then, another study identified a causative role for MYO15A gene mutation in DFNB3[4].MYO15A have 66 exons spanning 71 kb of DNA on chromosome 17p11.2[5].
The MYO15A mRNA transcript encodes a 3530 amino acid protein (myosin XVa), which has MyTh4 (Myosin-Tail like Homology region 4) domains, FERM (4.1 protein, Ezrin, Radixin, and Moesin) motifs, a SH3 (Src Homology 3) domain, and the PDZ domain. Myosin-XVa is a critical protein for tip localization of whirlin and differential elongation of hair-cell stereocilia and organization of actin within the hair cells of cochlea so Myosin-XVa is an important element in normal auditory function[6].
There are several linkage analysis studies about mutations of MYO15A causing ARNSHL in consanguineous families from specific countries, such as Pakistan, Turkey, and Iran[7-9]. Mutations of MYO15A at the DFNB3 locus are the second cause of autosomal recessive non-syndromic deafness in Iranian population[7, 9]. In the present study, we reported a novel MYO15A mutation identified by clinical exome sequencing in a consanguineous Iranian family with ARNSHL. To the best of our knowledge, this mutation has not been reported in any database.
Materials and methods
A 22 years old female with hearing loss was referred to Medical Genetic Department, Urmia Medical University, for detection of any possible hereditary hearing loss mutation. Parents were consanguineous with F=1/16 (first cousin) and clinical examination exclude dysmorphic features. Audiometric records were compatible with sensorineural hearing loss, so non-syndromic sensorineural hearing loss was confirmed.
Molecular analysis was performed after obtaining informed consent. Sanger sequencing for the common deafness genes, that is, GJB2 and GJB6, was negative. Clinical exome sequencing was performed on a single proband case. After preliminary detection of mutation by Clinical exome sequencing, PCR amplification and Sanger sequencing were performed to verify that the identified mutation co-segregate with the phenotype in the studied family. In addition, detected mutation was searched in healthy controls database for the same ethnic group (Iranome; http://www.iranome.ir/).
Evolutionary conservation of the sequences and structures of the proteins and nucleic acids was assessed Using the 1000 Genomes Project database, and the ExAC (Exome Aggregation Consortium) browser.
Results
A novel homozygous mutation c.9611_9612+8del (p.Leu3204Cysfs*17) found at exon 58 of MYO15A in a consanguineous Iranian family with a case of non-syndromic sensorineural hearing loss. (fig1) This mutation creates a shift in the reading frame starting at codon 3204. The new reading frame ends in a stop codon 16 positions downstream. The deletion is in close proximity to the highly conserved donor splice site of exon 58. This mutation has been confirmed by Sanger sequencing. It is classified as likely pathogenic (class2) according to the recommendations of ACMG. Using the 1000 Genomes Project database and the ExAC (Exome Aggregation Consortium) browser, candidate pathogenic variants were defined as splice-site and frameshift mutation.
The mutation was determined to be heterozygous in her parents. The c.9611_9612+8del was not found in healthy controls database for the same ethnic group (Iranome; http://www.iranome.ir/). This novel mutation is predicted to disrupt the function of the myosin XVa protein, which is integral to the mechanosensory and neurosensory activity of hair cells in the inner ear.
The alignment of MYO15A from different species of human, chimpanzee, monkey and cattle was analyzed. The result proved that this region was conservative among multiple species which highly suggesting that these residues are important for the proper protein function.