Department of Nursing, Shoushtar Faculty of Medical Sciences, Shoushtar, Iran
Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
Department of ENT, Faculty of Medicine, Guilan University of Medical Sciences, Guilan, Iran
P.O. BOX: 64516-84534
Department of Nursing
Shoushtar Faculty of Medical Sciences
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Ghanbari Mardasi Farideh,
Mohammadi Asl Javad,
Najafvand Zadeh Marziye.
Identification of Novel PTPRQ and MYO1A Mutations
in An Iranian Pedigree with Autosomal
Recessive Hearing Loss.
Autosomal recessive non-syndromic hearing loss (ARNSHL) is defined as a genetically heterogeneous disorder. The
aim of the present study was to screen for pathogenic variants in an Iranian pedigree with ARNSHL. Next-generation
targeted sequencing of 127 deafness genes in the proband detected two novel variants, a homozygous missense variant
in PTPRQ (c.2599 T>C, p.Ser867Pro and a heterozygous missense variant in MYO1A (c.2804 T>C, p.Ile935Thr),
both of which were absent in unaffected sibs and two hundred unaffected controls. Our results suggest that the
homozygous PTPRQ variant maybe the pathogenic variant for ARNSHL due to the recessive nature of the disorder.
Nevertheless, the heterozygous MYO1A may also be involved in this disorder due to the multigenic pattern of ARNSHL.
Our data extend the mutation spectrum of PTPRQ and MYO1A, and have important implications for genetic counseling
in unaffected sibs of this family. In addition, PTPRQ and MYO1A pathogenic variants have not to date been reported
in the Iranian population.
Hearing impairment is one of the most common
sensorineural disorders in humans, affecting
approximately one in 500-1,000 newborns. Hereditary
hearing impairments are mainly transmitted in an autosomal
dominant or recessive fashion (1) with mitochondrial (2) or
X-linked (3) inheritance reported in frequently. Considering
the isolated forms, about 80% of hereditary deafness cases
manifest as autosomal recessive non-syndromic hearing
loss (ARNSHL) (4). To date, more than 100 genes have
been implicated in ARNSHL (5).
Molecular diagnosis plays a key role in clinical
management, prognosis evaluation and prenatal diagnosis
(PND) for ARNSHL families (6). However, the genetic
heterogeneity of hearing impairment had undermined
genetic diagnosis in most cases until recently. With the
advent of next-generation sequencing (NGS) technology,
heterogeneous disorders are now open to routine genetic
testing and comprehensive genetic analysis. Targeted
NGS of the identified deafness genes (a “gene panel”
that generally covers the exons and flanking intronic
sequences) can provide a basis for a broad first-step
study of pathogenic variants in ARNSHL (7). We thus
aimed to screen the deafness gene panel in a proband
with ARNSHL and of Iranian origin. Herein, we report
two novel missense pathogenic variants in PTPRQ and
MYO1A, both of which may explain the ARNSHL
phenotype in the proband.
The proband is a 23-year-old Iranian male with a clinical
diagnosis of hearing impairment (Fig .1A,). No exact
complications have been reported during his perinatal
period. However, at age of 21 months, his mother
suspected hearing loss because of his poor response to
sound. He was born from a consanguineous marriage (first
cousin unaffected parents). There was no family history
of inherited diseases such as ARNSHL or congenital
malformations in his pedigree. Two hundred unrelated
subjects of Iranian origin with normal hearing were
screened for the pathogenic variants as controls. Written
informed consent was obtained from all participants
according to the guidelines of the Ethics Committee of the
Ministry of Health and Medical Education of Iran.
Blood samples were collected from the proband and
his parents. Genomic DNA was extracted from blood
samples of all participants using the standard salting
out method (8). Targeted NGS was carried out by using
a custom designed NimbleGen chip capturing 127
hearing impairment genes including but not limited to
PTPRQ, GJB6, MYO1A, MYO7A, SLC26A4, and MTRNR1
(BGI-Clinical Laboratories, China). The genomic
region containing the variant were amplified (primer
sequences are available upon request) in 25 µL volumes
and 35 cycles: 95°C for one minute, 65°C for 40 seconds
and 72°C for one minute and then the polymerase chain
reaction (PCR) product was sequenced with direct sanger
sequencing carried out with automated DNA sequencer
(ABI3130, Applied Biosystems, USA) (validation with a
second independent sample of DNA) to confirm presence
of potential pathogenic variants in the proband and his
parents for segregation analysis.
The frequency of the detected variants was checked in
the 1000 genomes database (http://WWW.1000genomes.
org/.). Next, in silico functional prediction of the
missense variants were performed with bioinformatics
tools including Sorting Intolerant from Tolerant (SIFT)
(9), Polymorphism Phenotyping V2 (PolyPhen2) (10) and
Mutation Taster (11).
All genomic data analysis including read alignment,
variant calling and novel mutation identification was
undertaken by BGI that detected two novel variants in
PTPRQ and MYO1A co-segregating in the family. The
variant in exon 17 of PTPRQ (c.2599T>C) results in a
serine to proline substitution at codon 867 (Ser867Pro)
(Fig .1B,). The second variant was found in exon 26 of
MYO1A (c.2804 T>C) (Fig .1C,), leading to an isoleucine to
threonine substitution (Ile935Thr). Both missense variants
were predicted to be pathogenicity the three prediction tools
(Table 1,). Reported mutations in PTPRQ and MYO1A are
summarized in Table 2, and 3 respectively. Interestingly,
no pathogenic variants were identified in the other 125
genes in the proband. The two detected variants were
confirmed by sanger sequencing. Both missense variants
alter highly evolutionary conserved amino acids (Fig .1D,
E,). To confirm pathogenicity, presence of the two variants
was checked in unaffected individuals in the pedigree.
The unaffected parents and one of his sisters (II-3) were
heterozygous for the PTPRQ variant while the MYO1A
variant was only identified in the mother in a heterozygous
state. Both variants were not detected in the other sister
(II-2) and the 200 healthy controls of Iranian origin.
Figure 2 shows the locations of these variants.
CP; Cytoplasmic domain, EC; Extracellular domain, and AR; Autosomal recessive.
- Genetic analysis of the ARNSHL proband. A. Pedigree of family
B with ARNSHL, the proband is denoted in black. Partial sequences
of B. PTPRQ, C. MYO1A in the proband showing that homozygous
mutation (c.2599T>C) in PTPRQ and the heterozygous mutation
(c.2804 T>C) in MYO1A, both co-segregating with the phenotype.
Mutated nucleotides are marked with vertical lines (black). Protein
alignment shows conservation of residue D. 867 in PTPRQ, and E.935
in MYO1A across seven and eight species respectively. These
two novel mutations occur at evolutionarily conserved amino acid
positions marked with vertical lines (black).
- Diagram structure of PTPRQ and Myosin-IA proteins. Schematic of
A. PTPRQ and B. Myosin-IA proteins show the locations of the pathogenic
variants in humans. The two novel mutations reported in this study are
shown in red font (p.Ser867Pro and p.Ile935Thr).
TH1; Class I myosin tail homology, AD; Autosomal dominant, and AR; Autosomal recessive.
Here we report two novel missense variants in PTPRQ
and MYO1A in an Iranian family displaying hearing
loss. Protein Tyrosine Phosphatase, Receptor Type Q
(PTPRQ) is a stereociliar membrane protein, composed
of three domains which include an extracellular domain
(containing 18 fibronectin III repeats), a membrane
spanning domain (trans membrane domain) and a
cytoplasmic domain (phosphatase domain) (12-14). It
plays key roles in cell shape changes, regulation of actin
filament organization and formation of stereocilia in hair
cells of the inner ear (15) with its loss or malfunction
resulting in shaft connector malformation of hair cell
The novel homozygous PTPRQ variant detected in the
proband is located in the fibronectin type III-9 domain
(extracellular domain). This extracellular domain is able
to bind ligands including extracellular proteins, collagen
and heparin as well as ligands on the cell (17-19). The
wild-type residue is polar while the mutant residue is
non-polar, thus likely to affect PTPRQ interactions with
Additionally, this is the first PTPRQ variant found in
an Iranian population. To date, 9 variants in PTPRQ have
been reported. All PTPRQ variants previously reported
were detected in prelinguistic or congenital hearing loss
patients (20). The proband in this study had congenital
hearing loss, consistent with previous reports. Of the 9
reported PTPRQ variants, five were missense variants in
the extracellular (EC) domain of which three were found
in a homozygous state [p.A457G in Morocco (12), and
p.D1042G and p.E1994G in China (21)] and two in a
heterozygous state [p.P56A and p.M1349T in Japan (20)].
Three were also nonsense variants in the EC domain that
were found in homozygous [p.Q429X in Palestine (13)
and p.Y497X in Holland (112)] or heterozygous [p.R421X
in Japan (20)] state. The ninth variant was a heterozygous
splice site variant (c.6453+3delA) detected in a Japanese
We also identified a novel heterozygous variant in
MYO1A as a potentially causative variant of congenital
ARNSHL in the proband. MYO1A encodes Myosin-
IA, a protein with 1043 amino acids, belonging to the
myosin super family (22, 23). MYO1A contains three
core domains, an N-terminal motor domain, a central
neck region made up of IQ motifs and a tail region.
MYO1A functions as an actin-based molecular motor
and is implicated in directing the movement of organelles
along the actin filaments (24).
Variants within this gene have been reported to cause
ARNSHL (25). To date, 10 recessive variants in MYO1A
have been shown to be associated with ARNSHL in
patients of Italian, German and Pakistani descent.
However, variants in MYO1A have not to date been
reported in the Iranian population.
The c.2804 T>C variant located in the C-terminal tail
homology-1 (TH1) domain, which is responsible for
membrane binding (26). Therefore, missense variants
that alter a nonpolar aliphatic amino acid to polar amino
acids with a hydroxyl group may modify the interaction
of the tail domain with membranous compartments and
alter its movement. Therefore this novel variant is likely
to negatively affect the function of the TH1 domain.
ARNSHL has an autosomal recessive inheritance pattern
and since neither parents nor the proband are homozygous,
it is unlikely to be causal in this case. However, this
variant might cause pathogenicity in case another variant
is acquired in future generations and result in compound
Our findings confirm that two novel variants in
PTPRQ and MYO1A may be causative of ARNSHL in a
consanguineous Iranian family. In conclusion, by using
NGS in this study, we show that this method can be useful
for detecting rare causative genetic variants in ARNSHL
patients, such as those detected in MYO1A and PTPRQ.
The authors thank the Milad Genetic Counseling Center
and all of the individuals for their participation in this
study. There is no financially support and conflict of
interest in this study.
F.T.; Study conception and design. F.Gh.M.; Acquisition
of data, analysis and interpretation of data, drafting
of manuscript, critical revision. S.T., M.N.Z., J.M.A.;
Analysis and interpretation of data. All authors read and
approved the final manuscript.
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