ArticleBioinformatics (Oxford, England)2020
Rhapsody: predicting the pathogenicity of human missense variants.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 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
51 citing papers in PubMed, 106 citations in OpenAlex.
- Regulated degradation of KCC2, a potassium-chloride co-transporter required for synaptic transmission and neurodevelopment.Channels (Austin, Tex.) · 2026Review
- Deep phenotyping of EHMT1 ankyrin repeat domain missense variants in Kleefstra syndrome by multi-tiered structural genomics analyses at atomic resolution.Human molecular genetics · 2026Article
- Clinical Discovery and Molecular Analysis of Two Novel MSH2 Gene Mutations (p.Ala771Gly and p.Val797Gly) in Saudi Colorectal Cancer Patients: Potential Implications for Tumorigenesis.Health science reports · 2026Article
- Pathogenicity Prediction of Missense Variations in Hereditary Cancer Genes.International journal of molecular sciences · 2026Article
- Population- and haplotype-dependent variation aroundJID innovations : skin science from molecules to population health · 2026Article
- AFrontiers in immunology · 2026Article
- Allosteric Autoregulation of Ferroptosis Suppressor Protein 1 Activity by its N-myristoylated Tail.Journal of molecular biology · 2025Article
- Article
- Accurate identification and mechanistic evaluation of pathogenic missense variants withProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Variant effect predictor correlation with functional assays is reflective of clinical classification performance.Genome biology · 2025Article
- Advancing Deep Variant Phenotyping of Mitochondrial Enzyme Complexes For Precision Medicine in Allogeneic Hematopoietic Stem-Cell Transplantation.Transplantation reports · 2025Article
- AFFIPred: AlphaFold2 structure-based Functional Impact Prediction of missense variations.Protein science : a publication of the Protein Society · 2025Article
- TITINdb2-expanding annotation and structural information for protein variants in the giant sarcomeric protein titin.Bioinformatics advances · 2025Article
- Pharmacological chaperones restore proteostasis of epilepsy-associated GABAPharmacological research · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Rapid discrimination between deleterious and benign missense mutations in the CAGI 6 experiment.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
- Influence of point mutations on PR65 conformational adaptability: Insights from molecular simulations and nanoaperture optical tweezers.Science advances · 2024Article
- Precise prediction of phase-separation key residues by machine learning.Nature communications · 2024Article
- Genotype-Phenotype Associations in an X-Linked Retinoschisis Patient Cohort: The Molecular Dynamic Insight and a Promising SD-OCT Indicator.Investigative ophthalmology & visual science · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
motivationThe biological effects of human missense variants have been studied experimentally for decades but predicting their effects in clinical molecular diagnostics remains challenging. Available computational tools are usually based on the analysis of sequence conservation and structural properties of the mutant protein. We recently introduced a new machine learning method that demonstrated for the first time the significance of protein dynamics in determining the pathogenicity of missense variants.
resultsHere, we present a new interface (Rhapsody) that enables fully automated assessment of pathogenicity, incorporating both sequence coevolution data and structure- and dynamics-based features. Benchmarked against a dataset of about 20 000 annotated variants, the methodology is shown to outperform well-established and/or advanced prediction tools. We illustrate the utility of Rhapsody by in silico saturation mutagenesis studies of human H-Ras, phosphatase and tensin homolog and thiopurine S-methyltransferase. AVAILABILITY AND IMPLEMENTATION: The new tool is available both as an online webserver at http://rhapsody.csb.pitt.edu and as an open-source Python package (GitHub repository: https://github.com/prody/rhapsody; PyPI package installation: pip install prody-rhapsody). Links to additional resources, tutorials and package documentation are provided in the 'Python package' section of the website. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What 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.