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The Manitoba Oculo-Tricho-Anal (MOTA) syndrome was first described in 1992. MOTA syndrome is a rare syndrome. MOTA syndrome has a clear genetic autosomal recessive inheritance pattern. The MOTA syndrome is related to FRAS1 (Fraser extracellular matrix complex subunit 1) related extracellular matrix 1 (FREM1) gene mutation, which can also cause genitourinary defects (including renal agenesis), nasal abnormalities and anorectal abnormalities. In our case, a pregnant woman whose fetus had been diagnosed during a routine mid-trimester ultrasound scan with unilateral renal agenesis and no other structural abnormalities delivered at 39 weeks by elective caesarean section. Unfortunately, the baby died shortly after delivery due to failed intubation. On post-mortem genetic analysis using whole genome sequencing, MOTA syndrome was diagnosed. Previous reports suggested that FREM1 mutations may contribute to upper airway malformations. This case highlights the need for genetic analysis to diagnose MOTA syndrome.