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Recent progress in genomic analysis has accelerated the analysis of chromosomal translocation\u2010breakpoints at the nucleotide level. Using a long\u2010read whole\u2010genome sequence, we analyzed the breakpoints of the cytogenetically balanced chromosomal translocation t(5;15)(q21;26.3), which was confirmed to be of de novo origin, in a patient with a neurodevelopmental disorder. The results showed complex rearrangements with seven fragments consisting of five breakpoint\u2010junctions (BJs). Four of the five BJs showed microhomologies of 1\u20133\u2010bp, and only one BJ displayed a signature of blunt\u2010end ligation, indicating chromothripsis as the underlying mechanism. Although the BJs did not disrupt any disease\u2010causing gene, the clinical features of the patient were compatible with <jats:italic>MEF2C<\/jats:italic> haploinsufficiency syndrome. Complex rearrangements were located approximately 2.5\u2010Mb downstream of <jats:italic>MEF2C<\/jats:italic>. Therefore, position effects were considered the mechanism of the occurrence of <jats:italic>MEF2C<\/jats:italic> haploinsufficiency syndrome.<\/jats:p>","DOI":"10.1002\/ajmg.a.63182","type":"journal-article","created":{"date-parts":[[2023,3,14]],"date-time":"2023-03-14T09:32:03Z","timestamp":1678786323000},"page":"1632-1638","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Breakpoint analysis for cytogenetically balanced translocation revealed unexpected complex structural abnormalities and suggested the position effect for <scp><i>MEF2C<\/i><\/scp>"],"prefix":"10.1002","volume":"191","author":[{"given":"Takeaki","family":"Tamura","sequence":"first","affiliation":[{"name":"Department of Pediatrics and Child Health Nihon University School of Medicine  Tokyo Japan"},{"name":"Division of Gene Medicine Graduate School of Medical Science, Tokyo Women's Medical University  Tokyo Japan"},{"name":"Department of Transfusion 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