Recurrent De Novo NAHR Reciprocal Duplications in the ATAD3 Gene Cluster Cause a Neurogenetic Trait with Perturbed Cholesterol and Mitochondrial Metabolism

Recent studies have identified both recessive and dominant forms of mitochondrial disease that result from ATAD3A variants. The recessive form includes subjects with biallelic deletions mediated by non-allelic homologous recombination. We report five unrelated neonates with a lethal metabolic disorder characterized by cardiomyopathy, corneal opacities, encephalopathy, hypotonia, and seizures in whom a monoallelic reciprocal duplication at the ATAD3 locus was identified. Analysis of the breakpoint junction fragment indicated that these 67 kb heterozygous duplications were likely mediated by non-allelic homologous recombination at regions of high sequence identity in ATAD3A exon 11 and ATAD3C exon 7. At the recombinant junction, the duplication allele produces a fusion gene derived from ATAD3A and ATAD3C, the protein product of which lacks key functional residues. Analysis of fibroblasts derived from two affected individuals shows that the fusion gene product is expressed and stable. These cells display perturbed cholesterol and mitochondrial DNA organization similar to that observed for individuals with severe ATAD3A deficiency. We hypothesize that the fusion protein acts through a dominant-negative mechanism to cause this fatal mitochondrial disorder. Our data delineate a molecular diagnosis for this disorder, extend the clinical spectrum associated with structural variation at the ATAD3 locus, and identify a third mutational mechanism for ATAD3 gene cluster variants. These results further affirm structural variant mutagenesis mechanisms in sporadic disease traits, emphasize the importance of copy number analysis in molecular genomic diagnosis, and highlight some of the challenges of detecting and interpreting clinically relevant rare gene rearrangements from next-generation sequencing data. Recent studies have identified both recessive and dominant forms of mitochondrial disease that result from ATAD3A variants. The recessive form includes subjects with biallelic deletions mediated by non-allelic homologous recombination. We report five unrelated neonates with a lethal metabolic disorder characterized by cardiomyopathy, corneal opacities, encephalopathy, hypotonia, and seizures in whom a monoallelic reciprocal duplication at the ATAD3 locus was identified. Analysis of the breakpoint junction fragment indicated that these 67 kb heterozygous duplications were likely mediated by non-allelic homologous recombination at regions of high sequence identity in ATAD3A exon 11 and ATAD3C exon 7. At the recombinant junction, the duplication allele produces a fusion gene derived from ATAD3A and ATAD3C, the protein product of which lacks key functional residues. Analysis of fibroblasts derived from two affected individuals shows that the fusion gene product is expressed and stable. These cells display perturbed cholesterol and mitochondrial DNA organization similar to that observed for individuals with severe ATAD3A deficiency. We hypothesize that the fusion protein acts through a dominant-negative mechanism to cause this fatal mitochondrial disorder. Our data delineate a molecular diagnosis for this disorder, extend the clinical spectrum associated with structural variation at the ATAD3 locus, and identify a third mutational mechanism for ATAD3 gene cluster variants. These results further affirm structural variant mutagenesis mechanisms in sporadic disease traits, emphasize the importance of copy number analysis in molecular genomic diagnosis, and highlight some of the challenges of detecting and interpreting clinically relevant rare gene rearrangements from next-generation sequencing data. Since its initial association with a neurological disorder,1Harel T. Yoon W.H. Garone C. Gu S. Coban-Akdemir Z. Eldomery M.K. Posey J.E. Jhangiani S.N. Rosenfeld J.A. Cho M.T. et al.Baylor-Hopkins Center for Mendelian GenomicsUniversity of Washington Center for Mendelian GenomicsRecurrent de novo and biallelic variation of ATAD3A, encoding a mitochondrial membrane protein, results in distinct neurological syndromes.Am. J. Hum. Genet. 2016; 99: 831-845Abstract Full Text Full Text PDF PubMed Scopus (84) Google Scholar it has become apparent that disruption of the ATAD3 cluster, and more specifically ATAD3A (MIM: 612316), is a significant cause of pediatric disease. Variants at this locus are associated with a wide phenotypic spectrum, including pontocerebellar hypoplasia,2Desai R. Frazier A.E. Durigon R. Patel H. Jones A.W. Dalla Rosa I. Lake N.J. Compton A.G. Mountford H.S. Tucker E.J. et al.ATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism.Brain. 2017; 140: 1595-1610Crossref PubMed Scopus (53) Google Scholar hereditary spastic paraplegia,3Cooper H.M. Yang Y. Ylikallio E. Khairullin R. Woldegebriel R. Lin K.-L. Euro L. Palin E. Wolf A. Trokovic R. et al.ATPase-deficient mitochondrial inner membrane protein ATAD3A disturbs mitochondrial dynamics in dominant hereditary spastic paraplegia.Hum. Mol. Genet. 2017; 26: 1432-1443Crossref PubMed Scopus (33) Google Scholar and a syndromic neurological disorder characterized by peripheral neuropathy, hypotonia, cardiomyopathy, optic atrophy, cerebellar atrophy, and seizures:1Harel T. Yoon W.H. Garone C. Gu S. Coban-Akdemir Z. Eldomery M.K. Posey J.E. Jhangiani S.N. Rosenfeld J.A. Cho M.T. et al.Baylor-Hopkins Center for Mendelian GenomicsUniversity of Washington Center for Mendelian GenomicsRecurrent de novo and biallelic variation of ATAD3A, encoding a mitochondrial membrane protein, results in distinct neurological syndromes.Am. J. Hum. Genet. 2016; 99: 831-845Abstract Full Text Full Text PDF PubMed Scopus (84) Google Scholar Harel-Yoon syndrome (HAYOS [MIM: 617183]). The different phenotypes can be attributed to a spectrum of disease-causing variants that includes bi-allelic hypomorphic variants, bi-allelic deletions, and monoallelic dominant-negative missense variants. Here, we report two de nov