Detecting the Difficult: An Intronic NPC1 Variant Hiding in Plain Sight

An illustration of the importance of manual data review for identifying rare intronic variants adjacent to homopolymers is presented here. A 14-year-old male with Niemann-Pick Type C disease confirmed biochemically was only found to have a heterozygous pathogenic variant by molecular analysis. A manual review of the Next Generation Sequencing (NGS) data identified a c.709C>T; p.Pro237Ser variant, which was likely not reported initially because it is consistently classified as benign or likely benign. A rare association of the c.709C>T variant with a second intronic NPC1 variant (c.1947 + 5G>C) leading to the use of a cryptic splice donor site has been reported before. Further evaluation with Sanger sequencing detected the c.1947 + 5G>C variant as the second causative variant in this patient. Detection of a second allelic change in autosomal recessive inborn errors of metabolism and other genetic disorders is vital in establishing a diagnosis, initiating new therapies, and testing at risk family members. The case presented here illustrates a rare intronic splice site NPC1 variant that may not be readily detected by current short-read NGS technologies due to the downstream homopolymers and should be evaluated regularly, especially in the presence of another heterozygous variant.