ArticleBioinformatics (Oxford, England)2019
A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- Functional reassessment of extended splice region variants in MYO7A with hearing loss and Usher syndrome.The Journal of pathology · 2026Article
- Comparative fine-mapping of breast cancer susceptibility loci using summary statistics methods and multinomial regression.medRxiv : the preprint server for health sciences · 2026Article
- Haplotype-Based Analysis of OCA2 Variants in Oculocutaneous Albinism.Pigment cell & melanoma research · 2026Article
- Genetic analysis of neurodegenerative diseases.The Journal of clinical investigation · 2026Review
- 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
- A practical framework for predicting splicing single nucleotide variants in exome sequencing.NAR genomics and bioinformatics · 2025Article
- Genetic spectrum of congenital cataract with optional ocular and multisystem abnormalities.BMC medical genomics · 2025Article
- Unveiling splicing disruptions due to common somatic variants in acute myeloid leukemia.Human genomics · 2025Article
- Distinct genetic patterns and natural history of OPA1-related auditory neuropathy in Chinese population.Orphanet journal of rare diseases · 2025Article
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- Exploring NEK1 genetic variability in Italian amyotrophic lateral sclerosis patients.Journal of neurology · 2025Article
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- Clinical and Genetic Characteristics of 18 Patients from Southeast China with ABCA4-Associated Stargardt Disease.International journal of molecular sciences · 2025Article
- Bi-allelic variants in three genes encoding distinct subunits of the vesicular AP-5 complex cause hereditary macular dystrophy.American journal of human genetics · 2025Article
- Detection of mRNA Transcript Variants.Genes · 2025Review
- Discordance between a deep learning model and clinical-grade variant pathogenicity classification in a rare disease cohort.NPJ genomic medicine · 2025Article
- Exploring the role of splicing in TP53 variant pathogenicity through predictions and minigene assays.Human genomics · 2025Article
- Profiling of pathogenic variants in Japanese patients with sarcoglycanopathy.Orphanet journal of rare diseases · 2025Article
- Case Report: Evaluation ofFrontiers in medicine · 2025Article
- Stepwise Diagnostic Strategy Integrating Long-Read Sequencing for the Interpretation of Phenotype-Genotype Discordance in Dystrophinopathy.The application of clinical genetics · 2025Article
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Authors and funding
10 authors.
Funding
Abstract
summaryAssessing the pathogenicity of genetic variants can be a complex and challenging task. Spliceogenic variants, which alter mRNA splicing, may yield mature transcripts that encode non-functional protein products, an important predictor of Mendelian disease risk. However, most variant annotation tools do not adequately assess spliceogenicity outside the native splice site and thus the disease-causing potential of variants in other intronic and exonic regions is often overlooked. Here, we present a plugin for the Ensembl Variant Effect Predictor that packages MaxEntScan and extends its functionality to provide splice site predictions using a maximum entropy model. The plugin incorporates a sliding window algorithm to predict splice site loss or gain for any variant that overlaps a transcript feature. We also demonstrate the utility of the plugin by comparing our predictions to two mRNA splicing datasets containing several cancer-susceptibility genes. AVAILABILITY AND IMPLEMENTATION: Source code is freely available under the Apache License, Version 2.0: https://github.com/Ensembl/VEP_plugins. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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