ArticleJournal of human genetics2016
IntSplice: prediction of the splicing consequences of intronic single-nucleotide variations in the human genome.
Article in Journal of human genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- Genome-wide functional annotation and interpretation of splicing variants: toward RNA-targeted therapies.Journal of human genetics · 2025Review
- SRSF6 and SRSF1 coordinately enhance the inclusion of humanNAR molecular medicine · 2025Article
- Targeted Next-Generation Sequencing in Rare Diseases.Methods in molecular biology (Clifton, N.J.) · 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
- Identification and characterization of a novel intronic splicing mutation in CSF1R-related leukoencephalopathy.CNS neuroscience & therapeutics · 2024Article
- Benchmarking splice variant prediction algorithms using massively parallel splicing assays.Genome biology · 2023Article
- Article
- The role of Rapsyn in neuromuscular junction and congenital myasthenic syndrome.Biomolecules & biomedicine · 2023Review
- Novel Mutation in the FelineAnimals : an open access journal from MDPI · 2023Article
- Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies.BMC bioinformatics · 2022Article
- What's Wrong in a Jump? Prediction and Validation of Splice Site Variants.Methods and protocols · 2021Review
- Genetic analysis of 39 erythrocytosis and hereditary hemochromatosis-associated genes in the Slovenian family with idiopathic erythrocytosis.Journal of clinical laboratory analysis · 2021Article
- IntSplice2: Prediction of the Splicing Effects of Intronic Single-Nucleotide Variants Using LightGBM Modeling.Frontiers in genetics · 2021Article
- Four New Cases of SLC35A2-CDG With Novel Mutations and Clinical Features.Frontiers in genetics · 2021Article
- DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning.Nucleic acids research · 2020Article
- InMeRF: prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution.NAR genomics and bioinformatics · 2020Article
- Expanding the Boundaries of RNA Sequencing as a Diagnostic Tool for Rare Mendelian Disease.American journal of human genetics · 2019Article
- Functional reassessment of PAX6 single nucleotide variants by in vitro splicing assay.European journal of human genetics : EJHG · 2019Article
- Splicing mutations in human genetic disorders: examples, detection, and confirmation.Journal of applied genetics · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Precise spatiotemporal regulation of splicing is mediated by splicing cis-elements on pre-mRNA. Single-nucleotide variations (SNVs) affecting intronic cis-elements possibly compromise splicing, but no efficient tool has been available to identify them. Following an effect-size analysis of each intronic nucleotide on annotated alternative splicing, we extracted 105 parameters that could affect the strength of the splicing signals. However, we could not generate reliable support vector regression models to predict the percent-splice-in (PSI) scores for normal human tissues. Next, we generated support vector machine (SVM) models using 110 parameters to directly differentiate pathogenic SNVs in the Human Gene Mutation Database and normal SNVs in the dbSNP database, and we obtained models with a sensitivity of 0.800±0.041 (mean and s.d.) and a specificity of 0.849±0.021. Our IntSplice models were more discriminating than SVM models that we generated with Shapiro-Senapathy score and MaxEntScan::score3ss. We applied IntSplice to a naturally occurring and nine artificial intronic mutations in RAPSN causing congenital myasthenic syndrome. IntSplice correctly predicted the splicing consequences for nine of the ten mutants. We created a web service program, IntSplice (http://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice) to predict splicing-affecting SNVs at intronic positions from -50 to -3.
Indexed as
Identifiers
27009626What OpenQuestion holds
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.