ArticleFrontiers in genetics2023
Systematic errors in annotations of truncations, loss-of-function and synonymous variants.
Article in Frontiers in genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
- Alkaliphilic microbial cellulases: sources, structural insights, and bioengineering approaches for industrial applications.Archives of microbiology · 2026Review
- Proteome-Wide Analysis of Human Deletions.Proteins · 2026Article
- PON-Del predictor for sequence retaining protein deletions.PLoS computational biology · 2026Article
- There will always be variants of uncertain significance. Analysis of VUSs.NAR genomics and bioinformatics · 2024Article
- Article
- Pathogenic variants of human GABRA1 gene associated with epilepsy: A computational approach.Heliyon · 2023Article
- Nonsynonymous Synonymous Variants Demand for a Paradigm Shift in Genetics.Current genomics · 2023Review
- BTKbase, Bruton Tyrosine Kinase Variant Database in X-Linked Agammaglobulinemia: Looking Back and Ahead.Human mutation · 2023Article
- VariBench, new variation benchmark categories and data sets.Frontiers in bioinformatics · 2023Article
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Abstract
Description of genetic phenomena and variations requires exact language and concepts. Vast amounts of variation data are produced with next-generation sequencing pipelines. The obtained variations are automatically annotated, e.g., for their functional consequences. These tools and pipelines, along with systematic nomenclature, mainly work well, but there are still some problems in nomenclature, organization of some databases, misuse of concepts and certain practices. Therefore, systematic errors prevent correct annotation and often preclude further analysis of certain variation types. Problems and solutions are described for presumed protein truncations, variants that are claimed to be of loss-of-function based on the type of variation, and synonymous variants that are not synonymous and lead to sequence changes or to missing protein.
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