KEYWORDS
Microphthalmia, TENM3, Gene, Novel, Mutation, Coloboma
Introduction:
Microphthalmia, anophthalmia, and coloboma (MAC) display a range of MAC
ocular malformations [1]. The conditions of MAC are mostly related
to further ocular and non-ocular anomalies, demonstrating the gene
association accountable for several processes of development. It is
reported that almost 33% of reported cases affected with MAC are
syndromic and have abnormalities such as the craniofacial, renal,
genital, cardiac, brain, skeletal, etc. [2].
Anophthalmia (AO), MIM 206900, and microphthalmia (MO), MIM 309700, are
the worst congenital deformities of the eye in terms of severity, with a
prevalence of around 1 in 30,000 and 1 in 7,000 births, in turn
[3]–[5]. AO refers to the complete absence of the optic tissue
structure [6], [7], or the structures of visible ocular with
remnants that can be detected histologically [8]. MO is defined as a
decrease in the ocular globe size (total axial length of <19mm
in 1-year-old children and <21mm in adults) [6], [9],
[10].
These defects can be syndromic or isolated [11], [12], and may
occur unilateral or bilateral [6] with abnormalities occurring in
the vitreous (persistent fetal vasculature), lens (congenital cataract),
anterior segment (sclerocornea or Peters anomaly, microcornea, iris
coloboma), and/or posterior segment (optic coloboma) [13]–[17].
MO can be categorized into simple MO and complex MO based on the
presence of other ocular malformations or systemic diseases. The simple
MO is defined as an eye reduced in size but with normal shape, except
for the short axial length. [10] In comparison, the complex MO
occurs along with other eye deformities, such as chorioretinal coloboma,
iris coloboma, retinal coloboma, and persistent fetal vasculature
[12], [14], [18], [19].
Based on epidemiological studies, AO and MO have both heritable and
environmental causes, with genetic defects being the majority of common
causes [12], [14], [19], [20]. Beyond 30 genes are
associated with the non-syndromic AO and MO pathogenesis, the main
causative of which are RAX (MIM 601881), OTX2 (MIM
600037), PAX6 (MIM 607108), FOXE3 (MIM 6011094) [14],
[20], and SOX2 (MIM 184429) [21].
Based on the reports, several chromosomal abnormalities such as trisomy
13, mosaic trisomy 9, del7p15.1-p21.1, del14q22.1q23.2, delXp22.3,
del16p11.2, del16q11.2q12.2, dup10q24.31, and dup15q11.2q13.1, and also
some point mutations are involved in MO. The rearrangement of
chromosomes has been identified mainly related to syndromic MO, while
single-nucleotide variants could be detected in both non-syndromic and
syndromic forms [20], [22]. As several genes are involved in
most cases of chromosomal rearrangements, the resulting disorder is
usually syndromic, while disorders caused by point mutations can be
syndromic or non-syndromic, depending on the type of mutations and
involved genes. Due to the incidence of de novo mutations, incomplete
penetrance, mosaicism, and sporadic occurrence, genetic counseling is
not easy[3].
In this study, we investigated the genetic basis of microphthalmia in an
affected Iranian proband and reviewed the reported spectrum of the TENM3
gene mutations involved in this disorder.
Material and methods:
A 32-year-old symptomatic male with mild intellectual disability,
bilateral decrease in the ocular globe size, and coloboma living in Sari
city of Iran diagnosed as having bilateral colobomatous microphthalmia
based on his clinical and paraclinical features. His parents were first
cousins, and there was a positive family history in his pedigree. First
cousin of our patient’s father (case III-3) is also affected by Mo and
Coloboma, without intellectual disability (The patient did not consent
to the genetic test). After genetic counseling and drawing the familial
pedigree (Figure 1), the proband gave his informed consent before the
inclusion in this experiment. DNA extraction was done from whole blood
using standard extraction methods. Human whole-exome enrichment was
performed using Twist Human Core Exome Kit, and the library was
sequenced on Illumina platform with a raw coverage of 260X and mean
on-target coverage of 105X, performed by CeGaT GmbH, Germany. Only data
related to the 35 genes of interest were extracted for further analysis
(Name of these genes and their inheretence patterns are mentioned in
Table 1 based on OMIM databases). Our panel of 35 genes is based on the
genes listed in the OMIM Database for this disease, including genes that
cause the isolated disease and genes that cause the syndromic type. For
each disease, a panel of genes is introduced in the OMIM database, and
in the study of that disease, all those genes are examined, whether they
are the cause of syndromic or cause of isolated type. On the other hand,
because it was possible that the patient’s intellectual disability was
not associated with microphthalmia, we examined both isolated and
syndromic-type causative genes. Nearly all exons and flanking 10bp in
these genes were detected and analyzed. The NGS method’s analytical
sensitivity and specificity used in this assay to detect single point
mutations and small indels (within 20bp) are assumed to be
>95%.