Additive effect of frequent polymorphism and rare synonymous variant alters splicing in twin patients with Niemann-Pick disease type C

Abstract

Niemann-Pick disease type C (NP-C) (OMIM#257220) is a rare lysosomal storage disorder caused by pathogenic variants in either the NPC1 or NPC2 genes. It manifests with a wide spectrum of clinical symptoms and variable age of onset. We studied the impact of the frequent polymorphic variant c.2793 C > T (p.Asn931 = ), located in the donor splice site (SS) of NPC1 exon 18 on the penetrance of the rare synonymous variant c.2727 C > T (p.Cys909 = ), identified in two 55 y.o. twins with an adult onset form of NP-C. The patients' diagnosis was supported by biochemical analysis and positive filipin test. Analysis of the patients' cDNA showed that the c.2727 C > T variant leads to cryptic donor SS activation and frameshift deletion in the NPC1 exon 18. However, the minigene assay demonstrated that this exon shortening takes place only in the presence of the frequent polymorphic variant c.2793 C > T. Results of the transcript specific qPCR showed that only the presence in the NPC1 exon 18 of both variants leads to significant decrease of wild type (WT) transcript isoform.

Understanding the phenotypic variability in Niemann-Pick disease type C (NPC): a need for precision medicine

“…As a result, the mRNAs and the protein were undetectable 143 , 144 . In addition to frameshift variants, splicing defects exist in NPC and many other LSDs, such as Fabry, Pompe, and mucopolysaccharidosis type II 145 – 147 . Usually, variations that affect splicing occur in splicing regulatory sequences in the intronic and exonic regions 145 , and in this respect, it is important to note that even exonic variants that do not change the codon usage (i.e., same sense variants can also affect the splicing process 148 .…”

“…In addition to frameshift variants, splicing defects exist in NPC and many other LSDs, such as Fabry, Pompe, and mucopolysaccharidosis type II 145 – 147 . Usually, variations that affect splicing occur in splicing regulatory sequences in the intronic and exonic regions 145 , and in this respect, it is important to note that even exonic variants that do not change the codon usage (i.e., same sense variants can also affect the splicing process 148 . Most of the reported NPC1 splicing variants are in the intronic regions, except for six variants located in exons 14, 17, 19, 22, and 24 (c.1553 G > A, c.2292 G > A c.2599c>T, c.2911 G > C, c.3422 T > G and c.3754 G > C) 145 .…”

“…Usually, variations that affect splicing occur in splicing regulatory sequences in the intronic and exonic regions 145 , and in this respect, it is important to note that even exonic variants that do not change the codon usage (i.e., same sense variants can also affect the splicing process 148 . Most of the reported NPC1 splicing variants are in the intronic regions, except for six variants located in exons 14, 17, 19, 22, and 24 (c.1553 G > A, c.2292 G > A c.2599c>T, c.2911 G > C, c.3422 T > G and c.3754 G > C) 145 . To this date, variants in the NPC2 gene capable of affecting pre-mRNA splicing are less frequent; nonetheless, three intronic splicing variants have been reported in one study (IVS1 + 2 T > C; IVS2 + 5 G > A; IVS3 + 6 T > G).…”

“…In this area, Bychkov and colleagues 145 studied the impact of the frequent polymorphic variant c.2793 C > T, located in the donor splice site of NPC1 exon 18 on the rare synonymous variant c.2727 C > T, identified in two twins of 55 years old with adult-onset NPC. The variant leads to cryptic donor SS activation and frameshift deletion in the NPC1 exon 18.…”