O2081: Evaluation of Copy Number Losses in the MBD5 5’-untranslated Region: Expression Matters

Background: Diagnostic genomic tools, specifically chromosomal microarray analysis (CMA) and clinical exome sequencing (CES), play an essential role in diagnosing the subset of the pediatric population with multiple congenital anomalies and neurodevelopmental disorders. CMA and CES are the first-tier tests for diagnosing children with pathogenic copy number variants (CNV) or single nucleotide variants (SNV). While these tools are powerful, due to the inherent nature of these tests, they often neglect an essential region of a gene: the 5’untranslated region (5’UTR), which is critical in regulating gene transcription. We hypothesize that some variants in the 5’UTR alter gene expression. This altered gene expression may be responsible for the phenotype of some of these patients. Therefore, failure to interrogate the 5'UTR region may leave patients going underdiagnosed. Thus, we investigated CNVs identified in MBD5, a dosage-sensitive gene associated with MBD5-associated neurodevelopmental disorder (MAND). MAND is an umbrella term that describes a group of childhood-onset neurodevelopmental disorders (2q23.1 deletion syndrome, 2q23.1 duplication syndrome, and MBD5 SNVs) caused by pathogenic changes in MBD5 and share a common set of phenotypes.

Methods: A cohort of 42 individuals with deletions in the 5’ UTR region of MBD5 were collected from collaborating institution and referring diagnostic centers. In accordance with the local IRB protocols from Baylor College of Medicine, total RNA was isolated from lymphoblastoid cell lines from available patients and RNA quantification was performed. Lastly, phenotypic analysis of the patient cohort was performed.

Results: 42 children with CMA test results were identified with MBD5 5’UTR deletions. We separated these deletions into six groups based on what region of the 5’UTR was deleted. Patients with deletions of exon 1 revealed significant reduction of MBD5 mRNA expression levels. These patients had similar phenotype to classic 2q23.1 deletion syndrome patients.

Conclusion: This study confirms the importance of assessment of the 5’UTR in clinical genetics testing, particularly for dosage-sensitive genes, for we could be missing genetic diagnoses. The interpretation of 5'UTR variants and the diagnosis of MAND should be carefully considered and compared to the six groups of deletions described here. Finally, our study points to investigating the 5’UTR in dosage-sensitive genes to explore the potential for disease-causing variants fully. Comprehensive analysis of genomic variants must include the 5’UTR to gain near 100% coverage of dosage-sensitive genes in diagnostic testing.