Wei Wang1,2,*, Victor Wei Zhang3,4, Xiaoping Lan5, Juan Wang2, Yongchen Yang5, Chaoran Xia5, Mohen Xu5

1Department of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China 2Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China 3Baylor College of Medicine, Houston, USA

4AmCare Genomics Lab, GuangZhou, China

5Laboratory of Molecular Medicine, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China

*Corresponding author at: Department of Medical Genetics, Shanghai Children’s Hospital, Shanghai Jiaotong University, Shanghai, China.

E-mail address: angei200598@126.com (W. Wang).

Background: Inborn errors of metabolism (IEMs) are rarely caused by copy number variations. We identified triple troubles in a two and half year old girl born through in vitro fertilization. Initial visit revealed that she had history of failure to thrive, hypotonia, and development delay. Other clinical features included microcephaly and dysmorphic face. Brain MRI at age of one-year-old showed that her frontal lobes size was slightly atrophy. Mass spectrometry results from her blood and urine suggested 3-methylcrotonyl-CoA carboxylase deficiency (3- MCCD). Close examination revealed that she had 20 teeth with small size and yellow discoloration.

Methods: Medical Exome Sequencing covered with 4000 known diseasing genes that could cause clinically genetic diseases was used to screen suspected genetic causes on DNA extracted from her peripheral blood samples and parental samples for Trio analysis. Sanger sequencing and PCR were used to confirm the results.

Results: Three genetic abnormalities were identified in the case. A homozygous c.1630delA (p.R544Dfs*2) of MCCC1 gene was found. Her mother was confirmed to be heterozygous for this mutation. No point mutation of MCCC1 gene was detected on the parental chromosome. A de novo 1.36 Mb deletion of 3q27.1 encompassing MCCC1 gene was identified. This de novo deletion presumably occurs on the paternal chromosome. Compound heterozygous mutations of c.536C>G (p.S179*) and c.2686C>T (p.R896*) on WDR72 gene were identified. Her father is a carrier of c.536C>G (p.S179*) and her mother is a carrier of c.2686C>T (p.R896*).

Conclusion: A 1.36Mb deletion on 3q27.1 has never been reported before. However, 3 cases on the similar region had been reported to have development delay, microcephaly and dysmorphic features. The identified de novo deleted region harboring MCCC1 gene and one mutation of MCCC1 inherited from her mother together with consistent biochemical findings lead to the confirmed diagnosis of 3-MCCD. The diagnosis of amelogenesis imperfecta IIA3 caused by WDR72 gene was also established after closely clinical examination. The delineation of these mutational mechanisms provides additional insight for the diagnosis of IEMs. The triple troubles identified here present the advantage of NGS that could provide both CNV and SNV in single assay. The extra layer complexity has improved our understanding of the pathogenesis of complex diseases with unexplained clinical symptoms.

Key Words: Triple troubles, Inborn Errors of Metabolism, 3q27.1 deletion, 3-methylcrotonyl-CoA carboxylase deficiency, amelogenesis imperfecta IIA3, genetic causes, complex presentations.