WES was independently performed on individual S3, identifying a nucleotide change c.163−1G>A (chr14: 104,037,959 G>A) in APOPT1 by the same filtering strategy (Table 3, Figures 3A–3C). This variant is within the conserved consensus splice acceptor site of intron 1. Using muscle-derived individual S3 cDNA to study APOPT1 transcripts, we showed that exon 2 is completely skipped in the majority of transcripts, predicting the maintenance of the open reading frame for the synthesis of a 140-amino-acid-long species lacking approximately one-third of the wild-type protein (p.Val55_Lys120del). Low-level transcripts appeared to show partial retention of intron 1 (c.162+91_162+255) (Figure S3). No trace of normal APOPT1 mRNA was detected by this analysis.