Identification and Classification of Rare Variants in NPC1 and NPC2 in Quebec

Abstract

Niemann–Pick disease type C (NPC) is a treatable autosomal recessive neurodegenerative condition which leads to a variety of progressive manifestations. Despite most cases being diagnosed at a young age, disease prevalence may be underestimated, especially in adults, and interpretation of NPC1 and NPC2 variants can be difficult. This study aims to identify potential pathogenic variants in a large cohort of healthy individuals and classify their risk of pathogenicity to assist with future interpretation of variants. The CARTaGENE (CaG) cohort was used to identify possible variants of NPC1 and NPC2. Nine-hundred and eleven RNA samples and 198 exome sequencing were screened for genetic variants through a bio-informatic pipeline performing alignment and variant calling. The identified variants were analyzed using annotations for allelic frequency, pathogenicity and conservation scores. The ACMG guidelines were used to classify the variants. These were then compared to existing databases and previous studies of NPC prevalence, including the Tübingen NPC database. Thirty-two distinct variants were identified after running the samples in the RNA-sequencing pipeline, two of which were classified as pathogenic and 21 of which were not published previously. Furthermore, 46 variants were both identified in our population and with the Tübingen database, the majority of which were of uncertain significance. Ten additional variants were found in our exome-sequencing sample. This study of a sample from a population living in Quebec demonstrates a variety of rare variants, some of which were already described in the literature as well as some novel variants. Classifying these variants is arduous given the scarcity of available literature, even so in a population of healthy individuals. Yet using this data, we were able to identify two pathogenic variants within our population and several new variants not previously identified.

Estimated prevalence of Niemann–Pick type C disease in Quebec

“…Among the 1,109 data sets, 93 people are in both the RNA-seq and exome-seq groups, which gives us sequencing information on 1,016 distinct individuals. The cohort used in this study is representative of Quebec’s population based on sex, age and ethnicity 22 . Individuals in our cohort had no known neurological diseases.…”

“…The use of RNA-sequencing to identify variants has been proven to be reliable and enable the identification of high-quality variants 24 – 27 .The pipeline for identification and classification of NP-C variants was used as described before 22 . Briefly, the sequences from the 1016 individuals were aligned to the human reference genome version GRCh37.…”

STING trafficking as a new dimension of immune signaling

“…NPC1 is a lysosomal protein that mediates intracellular cholesterol trafficking and lipid homeostasis. Loss of function mutations in the NPC1 gene underlie 95% of NPC disease in humans ( Touma et al, 2021 ; Garver et al, 2007 ). Clinical manifestations of NPC disease include cerebellar ataxia, loss of Purkinje neurons, and progressive cognitive impairment.…”