Nanopore Sequencing Solves an Elusive Case of Sotos Syndrome

Sotos syndrome is a rare genetic disorder characterized by distinctive facial features, including a broad and prominent forehead, dolichocephaly, and learning disabilities ranging from mild to severe intellectual impairment. Affected individuals often show overgrowth in height and head circumference over two standard deviations. The syndrome is caused by haploinsufficiency of the NSD1 gene, with no evidence of genetic heterogeneity to date. Here we describe the unsolved case of a child of 4 years of age with a clinical diagnosis of Sotos syndrome. However, trio exome sequencing (ES) and exon chromosomal microarray (CMA) analysis excluded both small and large mutations in the NSD1 gene. As part of the Telethon Undiagnosed Programme, we used additional tools to investigate the possibility of new genes or elusive mutations that may have been missed by previous molecular diagnostic approaches. Therefore, we performed Nanopore long-read sequencing. This revealed a 447 bp insertion in exon 13 of the NSD1 gene. mRNA analysis confirmed in-frame skipping of exon 13 that encodes for two PHD domains. The genomic insertion shows 100% identity with an intronic region, although inverted, containing an AluSx1 element 2 kb upstream of the skipped exon, which may drive the event by masking the splice acceptor site of exon 13. Interestingly, this is the first case of Sotos syndrome linked to a pathogenic mechanism involving an insertion enclosing a transposable element generating a protein devoid of two PHDs, which are required for reading histone post-translational modifications.