ArticleGenome biology2010
Genomic features defining exonic variants that modulate splicing.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed, 118 citations in OpenAlex.
- Synonymous and non-synonymous variants at splice junctions can disrupt splicing and are frequently linked to disease associated loss of function genes.BMC genomics · 2025Article
- iSoMAs: Finding isoform expression and somatic mutation associations in human cancers.PLoS computational biology · 2025Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- Challenges Related to the Use of Next-Generation Sequencing for the Optimization of Drug Therapy.Handbook of experimental pharmacology · 2023Article
- SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing.Human mutation · 2022Article
- Transcriptome analysis provides critical answers to the "variants of uncertain significance" conundrum.Human mutation · 2022Review
- Disease-associated human genetic variation through the lens of precursor and mature RNA structure.Human genetics · 2022Review
- Genome interpretation using in silico predictors of variant impact.Human genetics · 2022Review
- Splicing mutations in the CFTR gene as therapeutic targets.Gene therapy · 2022Review
- In rice splice variants that restore the reading frame after frameshifting indel introduction are common, often induced by the indels and sometimes lead to organism-level rescue.PLoS genetics · 2022Article
- Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption.Nucleic acids research · 2021Article
- Case Report: A Synonymous Mutation inFrontiers in genetics · 2021Article
- Characterization of SynonymousFrontiers in oncology · 2021Article
- LEAP: Using machine learning to support variant classification in a clinical setting.Human mutation · 2020Article
- A Depletion of Stop Codons in lincRNA is Owing to Transfer of Selective Constraint from Coding Sequences.Molecular biology and evolution · 2020Article
- A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens.Frontiers in immunology · 2020Review
- Massive computational identification of somatic variants in exonic splicing enhancers using The Cancer Genome Atlas.Cancer medicine · 2019Article
- VIPdb, a genetic Variant Impact Predictor Database.Human mutation · 2019Article
- Predicting the impact of single nucleotide variants on splicing via sequence-based deep neural networks and genomic features.Human mutation · 2019Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundSingle point mutations at both synonymous and non-synonymous positions within exons can have severe effects on gene function through disruption of splicing. Predicting these mutations in silico purely from the genomic sequence is difficult due to an incomplete understanding of the multiple factors that may be responsible. In addition, little is known about which computational prediction approaches, such as those involving exonic splicing enhancers and exonic splicing silencers, are most informative.
resultsWe assessed the features of single-nucleotide genomic variants verified to cause exon skipping and compared them to a large set of coding SNPs common in the human population, which are likely to have no effect on splicing. Our findings implicate a number of features important for their ability to discriminate splice-affecting variants, including the naturally occurring density of exonic splicing enhancers and exonic splicing silencers of the exon and intronic environment, extensive changes in the number of predicted exonic splicing enhancers and exonic splicing silencers, proximity to the splice junctions and evolutionary constraint of the region surrounding the variant. By extending this approach to additional datasets, we also identified relevant features of variants that cause increased exon inclusion and ectopic splice site activation.
conclusionsWe identified a number of features that have statistically significant representation among exonic variants that modulate splicing. These analyses highlight putative mechanisms responsible for splicing outcome and emphasize the role of features important for exon definition. We developed a web-tool, Skippy, to score coding variants for these relevant splice-modulating features.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.