Clinical exome sequencing leads to the diagnosis of mitochondrial complex I deficiency in a family with global developmental delays, ataxia, and cerebellar and pons hypoplasia

Exome sequencing was performed on a 14 year-old female with familial ataxia, global developmental delays, and cerebellar and pons hypoplasia. The family history was remarkable for a 3 yearold sister with a similar phenotype. Nearly a decade of molecular, cytogenetic, and biochemical testing was uninformative. Exome sequencing revealed compound heterozygous alterations of the NUBPL gene (c.311T>C; p.L104P & c.815-27T>C). The c.311T>C missense alteration is located at a highly conserved amino acid. The c.815-27T>C alteration is located at a highly conserved nucleotide and previous in vitro analyses demonstrated splicing defects. The affected sister manifested both alterations; each parent carried one alteration. Alterations within the NUBPL gene occur in an autosomal recessive fashion in association with mitochondrial complex I deficiency syndrome (CI deficiency) (MIM_252010). The NUBPL gene was first discovered in association with disease in 2010 and has only been reported in two other families, both of which displayed remarkable clinical overlap with the family herein. Exome sequencing is an especially powerful tool to aid in the diagnosis of CI deficiency given the extreme clinical and genetic heterogeneity making establishing a clinical diagnosis exceedingly difficult. Further, the underlying mutation has not been discovered in about half of patients with CI deficiency, thought to be due to yet undiscovered associated genes. Diagnostic exome sequencing led to the successful identification of the NUBPL alterations and, after years of unsuccessful analyses, led to a molecular diagnosis for the family. METHODS  Genomic deoxyribonucleic acid (gDNA) was isolated from whole blood from the patients and sister. Samples were prepared using the SureSelect Target Enrichment System (Agilent Technologies, Santa Clara, CA). The enriched exome libraries were sequenced using paired-end, 100-cycle chemistry on the Illumina HiSeq 2000 (Illumina, San Diego, CA).  The Human Gene Mutation Database (HGMD; Stenson, 2009), OMIM, and several other databases were used to search for previously described gene mutations and polymorphisms. A molecular geneticist performed interpretive filtering based on the deleterious nature of the candidate alterations literature search and analysis of the relevance of the candidate genes’ function in relation to the patient’s phenotype.  Each candidate variant was analyzed by Sanger sequencing for mutation confirmation and co-segregation studies were performed for the family. Figure 2. c. 815-27C>T is a common branch point mutation Table 1: Variant Filtering Based on Inheritance Model & Interpretation P. Gray1, W. Zeng1, S. Tang1, J.J. Wei1, K. Gonzalez1, X. Li1, HM Lu1, H. Lu1, E.C. Chao1,2, V. Kimonis2 1) Ambry Genetics, Aliso Viejo, CA 2) Department of Pediatrics, University of California, Irvine, CA