Inherited glycophosphatidylinositol deficiency variant database and analysis of pathogenic variants.

Mol Genet Genomic Med 2019 Jul 24;7(7):e00743. Epub 2019 May 24.

CHU Sainte-Justine Research Center, University of Montreal, Montreal, Quebec, Canada.

Background: Glycophosphatidylinositol-anchored proteins (GPI-APs) mediate several physiological processes such as embryogenesis and neurogenesis. Germline variants in genes involved in their synthesis can disrupt normal development and result in a variety of clinical phenotypes. With the advent of new sequencing technologies, more cases are identified, leading to a rapidly growing number of reported genetic variants. With this number expected to rise with increased accessibility to molecular tests, an accurate and up-to-date database is needed to keep track of the information and help interpret results.

Methods: We therefore developed an online resource (www.gpibiosynthesis.org) which compiles all published pathogenic variants in GPI biosynthesis genes which are deposited in the LOVD database. It contains 276 individuals and 192 unique public variants; 92% of which are predicted as damaging by bioinformatics tools.

Results: A significant proportion of recorded variants was substitution variants (81%) and resulted mainly in missense and frameshift alterations. Interestingly, five patients (2%) had deleterious mutations in untranslated regions. CADD score analysis placed 97% of variants in the top 1% of deleterious variants in the human genome. In genome aggregation database, the gene with the highest frequency of reported pathogenic variants is PIGL, with a carrier rate of 1/937.

Conclusion: We thus present the GPI biosynthesis database and review the molecular genetics of published variants in GPI-anchor biosynthesis genes.

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Source
http://dx.doi.org/10.1002/mgg3.743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6625143PMC
July 2019
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RecQL4 cytoplasmic localization: Implications in mitochondrial DNA oxidative damage repair
Chi Z. et al.
International Journal of Biochemistry & Cell Biology 2012
Biosynthesis and deficiencies of glycosylphosphatidylinositol
Kinoshita T. et al.
Proceedings of the Japan Academy, Series B 2014
Alu‐mediated deletion of PIGL in a Patient with CHIME syndrome
Knight Johnson A. et al.
American Journal of Medical Genetics. Part A 2017

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