ArticleNAR genomics and bioinformatics2020
InMeRF: prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution.
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 29 citations in OpenAlex.
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- Comparison of genotypes and phenotypes for von Willebrand factor gene variants using Japanese genome database.Blood vessels, thrombosis & hemostasis · 2025Article
- A series of reviews in familial cancer: genetic cancer risk in context variants of uncertain significance in MMR genes: which procedures should be followed?Familial cancer · 2025Review
- Variant effect predictor correlation with functional assays is reflective of clinical classification performance.Genome biology · 2025Article
- Talin-1 variants associated with spontaneous coronary artery dissection (SCAD) highlight how even subtle changes in multi-functional scaffold proteins can manifest in disease.Human molecular genetics · 2024Article
- Enhancing Missense Variant Pathogenicity Prediction with MissenseNet: Integrating Structural Insights and ShuffleNet-Based Deep Learning Techniques.Biomolecules · 2024Article
- 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
- Dyssegmental dysplasia Rolland-Desbuquois type is caused by pathogenic variants in HSPG2 - a founder haplotype shared in five patients.Journal of human genetics · 2024Article
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- Identification of a buried β-strand as a novel disease-related motif in the human polysialyltransferases.The Journal of biological chemistry · 2024Article
- Myelin protein zero mutation-related hereditary neuropathies: Neuropathological insight from a new nerve biopsy cohort.Brain pathology (Zurich, Switzerland) · 2024Article
- MMPatho: Leveraging Multilevel Consensus and Evolutionary Information for Enhanced Missense Mutation Pathogenic Prediction.Journal of chemical information and modeling · 2023Article
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- A mutation in DOK7 in congenital myasthenic syndrome forms aggresome in cultured cells, and reduces DOK7 expression and MuSK phosphorylation in patient-derived iPS cells.Human molecular genetics · 2023Article
- Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications.Computational and structural biotechnology journal · 2023Review
- Genome interpretation using in silico predictors of variant impact.Human genetics · 2022Review
- PPVED: A machine learning tool for predicting the effect of single amino acid substitution on protein function in plants.Plant biotechnology journal · 2022Article
- Loss of Function Mutation in ELF4 Causes Autoinflammatory and Immunodeficiency Disease in Human.Journal of clinical immunology · 2022Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In predicting the pathogenicity of a nonsynonymous single-nucleotide variant (nsSNV), a radical change in amino acid properties is prone to be classified as being pathogenic. However, not all such nsSNVs are associated with human diseases. We generated random forest (RF) models individually for each amino acid substitution to differentiate pathogenic nsSNVs in the Human Gene Mutation Database and common nsSNVs in dbSNP. We named a set of our models 'Individual Meta RF' (InMeRF). Ten-fold cross-validation of InMeRF showed that the areas under the curves (AUCs) of receiver operating characteristic (ROC) and precision-recall curves were on average 0.941 and 0.957, respectively. To compare InMeRF with seven other tools, the eight tools were generated using the same training dataset, and were compared using the same three testing datasets. ROC-AUCs of InMeRF were ranked first in the eight tools. We applied InMeRF to 155 pathogenic and 125 common nsSNVs in seven major genes causing congenital myasthenic syndromes, as well as in
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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.