Utilizing RNA and outlier analysis to identify an intronic splice‐altering variant in AP4S1 in a sibling pair with progressive spastic paraplegia

We report a likely pathogenic splice‐altering AP4S1 intronic variant in two sisters with progressive spastic paraplegia, global developmental delay, shy character, and foot deformities. Sequencing was completed on whole‐blood messenger RNA (mRNA) and analyzed for gene expression outliers after exome sequencing analysis failed to identify a causative variant. AP4S1 was identified as an outlier and contained a rare homozygous variant located three bases upstream of exon 5 (NC_000014.8(NM_007077.4):c.295−3C>A). Confirmed by additional RNA‐seq, reverse‐transcription polymerase chain reaction, and Sanger sequencing, this variant corresponded with exon 5, including skipping, altered isoform usage, and loss of expression from the canonical isoform 2 (NM_001128126.3). Previously, loss‐of‐function variants within AP4S1 were associated with a quadriplegic cerebral palsy‐6 phenotype, AP‐4 Deficiency Syndrome. In this study, the inclusion of mRNA‐seq allowed for the identification of a previously missed splice‐altering variant, and thereby expands the mutational spectrum of AP‐4 Deficiency Syndrome to include impacts to some tissue‐dependent isoforms. Inclusion of mRNA‐seq analysis allowed for the identification of an intronic splice‐altering variant that suggests the loss of isoform 2 is sufficient to cause AP‐4 Deficiency Syndrome, and thereby expands the syndrome's mutational spectrum