ArticleNature genetics2023
SpliceVault predicts the precise nature of variant-associated mis-splicing.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed, 86 citations in OpenAlex.
- Rapid minigene workflow for functional reclassification of splicing variants in hereditary cancer diagnostics.Journal of medical genetics · 2026Article
- AAVC: An automated framework for high-accuracy ACMG-based variant classification.Genetics in medicine : official journal of the American College of Medical Genetics · 2026Article
- 'Missing' disease-causing variants in Alport syndrome.Nature reviews. Nephrology · 2026Review
- UniSplicer: A deep-learning framework for accurate splice-site prediction and splice-altering mutation detection across diverse taxa.Plant communications · 2026Article
- Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.Briefings in bioinformatics · 2026Review
- A mammalian genomic signature shaped by single nucleotide variants regulates transcriptome integrity and diversity.Genome biology · 2026Article
- A severe neurodevelopmental syndrome linked to a South Asian founder variant in the UFMylation adaptor CDK5RAP3.Acta neuropathologica · 2026Article
- Targeted long-read RNA sequencing for rare disease diagnosis and variant interpretation.Science advances · 2026Article
- Functional signatures of de novo GABBR1 and GABBR2 variants associated with neurodevelopmental disorders.NPJ genomic medicine · 2026Article
- Mapping the Non-Canonical Splicing Variants: Decrypting the Hidden Genetic Architecture of Idiopathic Male Infertility.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Generation of functional noncanonical donor splice sites by +2T variants in breast cancer susceptibility genes: impact on clinical interpretation.The Journal of pathology · 2026Article
- Experimental Mis-Splicing Assessment and ACMG/AMP-Guided Classification of 47International journal of molecular sciences · 2026Article
- Genome and transcriptome sequencing reveal pathogenic activation of a pseudoexon inGenetics in medicine open · 2026Article
- Article
- Titin-related familial dilated cardiomyopathy: factors associated with disease onset.European heart journal · 2025Observational
- Widespread naturally variable human exons aid genetic interpretation.Nature communications · 2025Article
- Functional analysis of BRCA1 and BRCA2 splicing variants using a minigene assay.Human genomics · 2025Article
- The utility of ultra-deep RNA sequencing in Mendelian disorder diagnostics.American journal of human genetics · 2025Article
- Genome-wide functional annotation and interpretation of splicing variants: toward RNA-targeted therapies.Journal of human genetics · 2025Review
- Unproductive alternative splicing of ATM exon 7: mapping of critical regulatory elements and identification of 34 spliceogenic variants.Journal of molecular medicine (Berlin, Germany) · 2025Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Even for essential splice-site variants that are almost guaranteed to alter mRNA splicing, no current method can reliably predict whether exon-skipping, cryptic activation or multiple events will result, greatly complicating clinical interpretation of pathogenicity. Strikingly, ranking the four most common unannotated splicing events across 335,663 reference RNA-sequencing (RNA-seq) samples (300K-RNA Top-4) predicts the nature of variant-associated mis-splicing with 92% sensitivity. The 300K-RNA Top-4 events correctly identify 96% of exon-skipping events and 86% of cryptic splice sites for 140 clinical cases subject to RNA testing, showing higher sensitivity and positive predictive value than SpliceAI. Notably, RNA re-analyses showed we had missed 300K-RNA Top-4 events for several clinical cases tested before the development of this empirical predictive method. Simply, mis-splicing events that happen around a splice site in RNA-seq data are those most likely to be activated by a splice-site variant. The SpliceVault web portal allows users easy access to 300K-RNA for informed splice-site variant interpretation and classification.
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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.