Abstract
Duchenne/Becker muscular dystrophy (DMD/BMD) is caused by variants in the X‐linked
DMD
gene—most commonly deletions, duplications, or point mutations, and only rarely by complex chromosomal rearrangements (CCRs). In this study, structural variant sequencing (SVseq) was applied to a 14‐year‐old male patient with DMD. Although the patient exhibited typical symptoms, conventional tests—including karyotype analysis, gene panel, whole‐exome sequencing (WES), and multiplex ligation–dependent probe amplification (MLPA)—were all negative. SVseq identified a novel complex rearrangement on the X chromosome, comprising a 974,456 bp inversion spanning the 5
′
UTR and Exons 1–2 of the
DMD
gene, flanked by two microdeletions of 7285 and 6468 bp (NC_000023.11:g.[32865334_32872619del;32872619_33847075inv33847075_33853543del]). This rearrangement disrupts the
DMD
coding sequence and is classified as a pathogenic variant. Short tandem repeat (STR) analysis confirmed the familial relationship, whereas PCR and Sanger sequencing precisely mapped the breakpoints, establishing that the mutation arose de novo in his mother and was maternally inherited. Reproductive interventions—including preimplantation genetic testing for monogenic disorders (PGT‐M) and second‐trimester prenatal diagnosis—enabled the successful birth of a healthy male child. SVseq demonstrated clear advantages over standard methods for detecting CCRs, highlighting its value in genetically elusive cases. We recommend SVseq as a complementary diagnostic tool for unresolved DMD cases where conventional testing does not explain the findings. This approach can enhance diagnostic yield and support informed family planning.