Classifying molecular phenotypes of G6PC variants for pathogenic properties and to guide therapeutic development

Due to advances in sequencing technologies, identification of genetic variants is rapid. However, the functional consequences of most genomic variants remain unknown. Consequently, variants of uncertain significance (VUS) that appear in clinical DNA diagnostic reports lack sufficient data for interpretation. Algorithms exist to aid prediction of a variant's likelihood of pathogenicity, but these predictions usually lack empiric evidence. To examine the feasibility of generating functional evidence in vitro for a given variant's role in disease, a panel of 29 coding sequence variants in the G6PC gene was assessed. G6PC encodes glucose-6 phosphatase enzyme, and reduction in its function causes the rare metabolic disease glycogen storage disease type 1a (GSD1a). Variants were heterologously expressed as fusion proteins in a hepatocyte-derived cell line and examined for effects on steady-state protein levels, biosynthetic processing, and intracellular distribution. The screen revealed variant effects on protein levels, N-linked glycosylation status, and cellular distribution. Of the eight VUS tested, seven behaved similar to wild-type protein while one VUS, p.Cys109Tyr, exhibited features consistent with pathogenicity for all molecular phenotypes assayed, including significantly reduced protein levels, alteration in protein glycosylation status, and abnormally diffuse protein localization pattern, and has recently been reported in a patient with GSD1a. Our results show that such a screen can add empiric evidence to existing databases to aid in diagnostics, and also provides further classification for molecular phenotypes that could be used in future therapeutic screening approaches for small molecule or gene editing strategies directed at specific variants.

Are GMI gangliosidosis and Morquio type B two different disorders or part of one phenotypic spectrum?

Monosialotetrahexosylganglioside (GMI) gangliosidosis and Morquio type B (MorB) are two lysosomal storage disorders (LSDs) caused by the same enzyme deficiency, β-galactosidase (βgal). GMI gangliosidosis, associated with GMI ganglioside accumulation, is a neurodegenerative condition characterized by psychomotor regression, visceromegaly, cherry red spot, and facial and skeletal abnormalities. MorB is characterized by prominent and severe skeletal deformities due to keratan sulfate (KS) accumulation. There are only a few reports on intermediate phenotypes between GMI gangliosidosis and MorB. The presentation of two new patients with this rare intermediate phenotype motivated us to review the literature, to study differences and similarities between GMI gangliosidosis and MorB, and to speculate about the possible mechanisms that may contribute to the differences in clinical presentation. In conclusion, we hypothesize that GMI gangliosidosis and MorB are part of one phenotypic spectrum of the same disease and that the classification of LSDs might need to be revised.

Accelerating structure-function mapping using the ViVa webtool to mine natural variation

Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of these data remain inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family, or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well-studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less-studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project ( http://snp-seek.irri.org/) and human genetic variation ( https://www.ncbi.nlm.nih.gov/clinvar/).

First Clinicogenetic Description of Parkinson's Disease Related to GBA Mutation S107L

Background

Mutations in the glucocerebrosidase gene (GBA) are a common genetic risk factor for Parkinson's disease (PD). Mutations in the N-terminus part of GBA are less commonly found in association with PD than those in the C-terminus. Phenotypic characterization of GBA-related PD has been challenging, in part attributed to differential impact of distinct GBA mutations.

Aim

To provide a phenotypic description of two patients with PD heterozygous for the GBA mutation S107L. The S107L mutation is located in the catalytic domain of glucocerebrosidase and has not previously been reported in patients with PD.

Methods

Motor and nonmotor symptoms (NMS) of PD were evaluated using established rating scales and questionnaires. The genotype was determined by Sanger sequencing.

Results

Two half-brothers, both heterozygous carriers of S107L, exhibited an early PD onset with several NMS.

Conclusions

In these patients, heterozygosity for S107L was associated with an early onset of PD with NMS.