ArticleGenome medicine2023
Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set.
Article in Genome medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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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.
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.
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Who cites it
34 citing papers in PubMed.
- From Pathogenicity to Mechanism: A Variant Interpretation Framework for Monogenic Epilepsy.Clinical genetics · 2026Article
- Functional effect predictions for ion channel missense variants using a protein language model.Journal of human genetics · 2026Article
- Prediction of human missense variant effects from functional evidence.Nature genetics · 2026Article
- Transcription-based identification of uncharacterized genes in the human immune response.European journal of human genetics : EJHG · 2026Article
- Bridging structure and function: artificial intelligence-based modelling of kidney proteins.Nature reviews. Nephrology · 2026Review
- Examining Genetic Variants Associated with FOXP1 Syndrome through Molecular Dynamics of Its DNA-Binding Domain and Self-Organizing Maps.Journal of chemical information and modeling · 2026Article
- Actually, what is a gain-of-function mutation?Genetics · 2026Article
- From variants to answers: The evolution of genetic counseling in IEI.Journal of human immunity · 2026Review
- Targeted deep sequencing identifies mosaicism in patients with immune dysregulation.The Journal of allergy and clinical immunology · 2026Article
- Genomics of drug target prioritization for complex diseases.Nature reviews. Genetics · 2026Review
- Interpreting the functional impact of genetic variants: The need for context qualifiers.American journal of human genetics · 2026Review
- Expanding the utility of variant effect predictions with phenotype-specific models.Nature communications · 2025Article
- Decoding missense variants pleiotropy in the immune GPCR P2RY8.Cell genomics · 2025Article
- Phenotypic pleiotropy of missense variants in human B cell confinement receptor P2RY8.Cell genomics · 2025Article
- Dominant negative ADA2 mutations cause ADA2 deficiency in heterozygous carriers.The Journal of experimental medicine · 2025Article
- Development of a genetic priority score to predict drug side effects using human genetic evidence.Nature communications · 2025Article
- Prevalence of loss-of-function, gain-of-function and dominant-negative mechanisms across genetic disease phenotypes.Nature communications · 2025Article
- Identification of a novelIntractable & rare diseases research · 2025Article
- PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context.Nature communications · 2025Article
- Classification of GBA1 variants and their impact on Parkinson's disease: an in silico score analysis.NPJ Parkinson's disease · 2025Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Gain-of-function (GOF) variants give rise to increased/novel protein functions whereas loss-of-function (LOF) variants lead to diminished protein function. Experimental approaches for identifying GOF and LOF are generally slow and costly, whilst available computational methods have not been optimized to discriminate between GOF and LOF variants. We have developed LoGoFunc, a machine learning method for predicting pathogenic GOF, pathogenic LOF, and neutral genetic variants, trained on a broad range of gene-, protein-, and variant-level features describing diverse biological characteristics. LoGoFunc outperforms other tools trained solely to predict pathogenicity for identifying pathogenic GOF and LOF variants and is available at https://itanlab.shinyapps.io/goflof/ .
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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.