ArticlePLoS computational biology2019
Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
44 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Variant effect predictors: a systematic review and practical guide.Human genetics · 2024Pooled it
- Calibration of in-frame indel variant effect predictors for clinical variant classification.bioRxiv : the preprint server for biology · 2026Article
- ClinGen Bayesian-Framework-Guided Interpretation of Compound HeterozygousDiagnostics (Basel, Switzerland) · 2026Article
- Proteome-Wide Analysis of Human Deletions.Proteins · 2026Article
- EpicTope: predicting and validating non-disruptive epitope tagging sites.Development (Cambridge, England) · 2026Article
- NEDAMSS syndrome-related truncating and missense mutations are associated with aberrant liquid-liquid phase separation of IRF2BPL.Nature communications · 2026Article
- Leveraging protein language models and a scoring function for indel characterization and transfer learning.Patterns (New York, N.Y.) · 2026Article
- PON-Del predictor for sequence retaining protein deletions.PLoS computational biology · 2026Article
- Literature-driven extraction and computational prediction of causal statements linking genetic variants to biological processes, pathways and phenotypes.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2026Article
- Novel polymorphisms and functional characterization of the prion protein gene in sparrows (Frontiers in veterinary science · 2026Article
- In-frame germline TP53 variant impairs p53 oligomerization and predisposes to cancer.Scientific reports · 2025Article
- Deciphering genetic adaptations of Old World camels through comparative genomic analyses across all camelid species.iScience · 2025Article
- Novel Insertion/Deletion Polymorphisms and Genetic Studies of the Shadow of Prion Protein (Animals : an open access journal from MDPI · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Global prevalence of hereditary thrombotic thrombocytopenic purpura determined by genetic analysis.Blood advances · 2024Article
- Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data.Genome biology · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- Novel In-Frame DeletionNeurology. Genetics · 2024Article
- Prediction of cancer driver genes and mutations: the potential of integrative computational frameworks.Briefings in bioinformatics · 2024Review
- InvestigatingArchives animal breeding · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Differentiation between phenotypically neutral and disease-causing genetic variation remains an open and relevant problem. Among different types of variation, non-frameshifting insertions and deletions (indels) represent an understudied group with widespread phenotypic consequences. To address this challenge, we present a machine learning method, MutPred-Indel, that predicts pathogenicity and identifies types of functional residues impacted by non-frameshifting insertion/deletion variation. The model shows good predictive performance as well as the ability to identify impacted structural and functional residues including secondary structure, intrinsic disorder, metal and macromolecular binding, post-translational modifications, allosteric sites, and catalytic residues. We identify structural and functional mechanisms impacted preferentially by germline variation from the Human Gene Mutation Database, recurrent somatic variation from COSMIC in the context of different cancers, as well as de novo variants from families with autism spectrum disorder. Further, the distributions of pathogenicity prediction scores generated by MutPred-Indel are shown to differentiate highly recurrent from non-recurrent somatic variation. Collectively, we present a framework to facilitate the interrogation of both pathogenicity and the functional effects of non-frameshifting insertion/deletion variants. The MutPred-Indel webserver is available at http://mutpred.mutdb.org/.
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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.