Two novel deep intronic variants cause Duchenne muscular dystrophy by splice-altering mechanism

•Two novel DMD intronic pathogenic variants were identified using targeted long-read sequencing.•Long-read sequencing accurately provides the breakpoint information for the two novel DMD intronic variants.•Pseudoexon activation is the mechanism underlying the two novel DMD intronic pathogenic variants. Duchenne muscular dystrophy (DMD) is a genetic disorder characterized by progressive muscle degeneration and weakness, due to mutations in the DMD gene, which encodes the dystrophin protein. While mutations within the coding regions of DMD have been extensively studied, recent focus has shifted to deep intronic variants for their potential impact on disease severity. Here, we characterize two deep intronic variants, c.8669-19_8669-24del and c.6439-1016_6439-3376del, in unrelated DMD patients. These variants were identified using targeted long-read sequencing on patients' DNA. RNA sequencing/reverse transcription polymerase chain reaction on RNA extracted from muscle biopsies revealed the presence of a pseudoexon or retention of part of the intron in the transcript, resulting in the introduction of premature termination codons. This study enhances our understanding of pseudoexon activation mechanisms in DMD and underscores the diverse genetic abnormalities contributing to the disease's complexity.