Exonisation of an Alu element in the 3'-UTR contributes to SRD5A2 deficiency

Steroid 5α-reductase deficiency is a rare autosomal recessive condition caused by mutations in the SRD5A2 gene that leads to a severe virilisation deficit of the external genitalia in individuals with a 46,XY karyotype. Here we report an adult 46,XY person with clinically confirmed steroid 5α-reductase deficiency. Sanger sequencing revealed a compound heterozygous, maternal, pathogenic c.692A > G; p.(His231Arg) variant and a very rare paternal c.*66T > G variant in the 3'-UTR. RT-PCR products of individual's derived genital skin fibroblasts revealed that only the maternal variant is expressed while the paternal variant could not be detected. PacBio RNA Isosequencing revealed that the variant c.*66T > G introduces a new strong splice donor site 66 nt after the canonical stop codon that is spliced to an inverted Alu sequence located 15 kb downstream. In all paternal, but none of the maternal transcripts, we found a new exon junction 66 nt after the stop codon within the 3'-UTR. Mammalian transcripts with an intron excision site > 55 nt downstream from a termination codon are subject to degradation by the nonsense-mediated decay (NMD) pathway. We conclude that the pathogenic maternal variant, together with the NMD-triggered downregulation of the paternal allele, is causative for the observed SRD5A2 deficiency.