Case reportDeep intronic variants introduce DMD pseudoexon in patient with muscular dystrophy

•Muscle mRNA analysis enables detection of deep intronic variants in DMD.•Common SNV facilitates the activation of a probable cryptic splice site.•Two SNVs (c.650-39575 A>C; c.650-39498 A>G) activate a pseudoexon in intron 7 of DMD.•Young boy with clinical BMD phenotype displays DMD genotype with frameshift mutation.

Dystrophinopathies are X-linked muscle diseases caused by mutations in the large DMD gene. The most common mutations are detected by standard diagnostic techniques. However, some patients remain without detectable mutation, most likely due to changes in the non-coding sequence. We report on a boy with complete absence of dystrophin in muscle biopsy but no causative mutation according to standard diagnostics. To search for deep intronic variations (DIV) in the DMD gene we isolated mRNA from muscle tissue and amplified overlapping cDNA fragments using RT-PCR. One cDNA product revealed an augmented fragment size showing an insertion of 77 bp between the exons 7 and 8 by sequencing. We sequenced the flanking sequences of gDNA and found two hemizygous single nucleotide variants (c.650-39575 A>C and c.650-39498 A>G) surrounding the inserted fragment. Both variants create cryptic splice sites which initiate the formation of a pseudoexon that produces a frameshift in the DMD gene.