Complete bilateral anophthalmia is the congenital absence of both eyes. Ambiguous genitalia is the condition in which the patient’s genitalia are incompletely developed or the baby has characteristics of both sexes. Pathogenic variants inSOX2 gene are associated with syndromic microphthalmia, type 3 (OMIM: 206900), with autosomal dominant inheritance pattern and with AEG syndrome (OMIM 600992). We report the case of a new born baby girl with bilateral anophthalmia and clitoris and labia minora agenesis, which originated from in vitro fertilization (IVF). Sequential genetic testing, QF-PCR, microarray and WES have been performed and DNA was obtained according to standard procedures. Whole exome sequencing (WES) identified a mutation in SOX2 (OMIM: 184429) gene, a heterozygous pathogenic variant, NM_003106.4: c.371dupA p. (Tyr125Valfs*14), highlighting the importance of this particular gene in embryogenesis, sexualization and the development of the visual function. It explains the clinical diagnosis of the patient. We have concluded that this particular mutation found in the SOX2 gene could be correlated to the pathological findings, although it was not reported before in the clinical databases. Furthermore, a prenatal testing algorithm would be very helpful. Additionally, we want to highlight the importance of a multidisciplinary team when diagnosing and managing the follow-up of a fetus with multiple malformation such as this particular case.
 

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