ArticleJournal of molecular biology2019
Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated?
Article in Journal of molecular biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 299 papers, 1 of them a synthesis that pooled it.
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
299 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A novel homozygous variant in the POLR1A gene: a complicated hereditary spastic paraplegia (c-HSP) or a hypomyelinating leukodystrophy type-27 (HLD27) phenotype?Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2026Pooled it
- Trial
- Computational identification and characterization of high-risk human KRAS nsSNPs: Impacting structure, ligand binding, and cancer prognosis.Journal, genetic engineering & biotechnology · 2026Article
- The anion channel GPR89 is a tumor-specific dependency in breast cancer.Nature communications · 2026Article
- Clinical and genetic spectrum of distal renal tubular acidosis in children: findings from Indian tubular disorders registry.Pediatric nephrology (Berlin, Germany) · 2026Article
- Comparative genomic analysis of oxytocin and oxytocin receptor genes in the family Equidae.Molecular biology reports · 2026Article
- High-coverage paleo-genome research identifies a pathogenic mutation on EXT1 in a Qing-period Chinese individual with multiple osteochondromas.Molecular genetics and genomics : MGG · 2026Article
- Article
- Multilocus sequence typing of the invasive pest Halyomorpha halys (Hemiptera: Pentatomidae) and associated endosymbiont reveals unexplored diversity.Insect science · 2026Article
- Novel SNPs in the leptin gene: implications for growth performance in cultured European sea bassJournal of veterinary research · 2026Article
- Machine Learning-Driven Simulations of the SARS-CoV-2 Fitness Landscape from Deep Mutational Scanning Experiments.Journal of chemical information and modeling · 2026Article
- Positional identification of a candidate gene for MALE STERILITY 2 (MS2) by linkage mapping and transcriptomic data in Cryptomeria japonica D. Don.BMC genomics · 2026Article
- Genomic and molecular characterisation of a KPC-producing Klebsiella pneumoniae clinical isolate resistant to meropenem-vaborbactam, imipenem-relebactam, and ceftazidime-avibactam.BMC genomic data · 2026Article
- Article
- VUStruct: A compute pipeline for high throughput and personalized structural biology.PLoS computational biology · 2026Article
- On the brink of emergence: an evolutionary approach to Influenza A virus H5N1 isolated from humans.Virus research · 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
- Convergent evolution increases boron transport through SNPs and tandem duplications atProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Phenotype-Driven Next-Generation Sequencing and Structure-Based In Silico Analysis Reveal Disease-Specific Diagnostic Yield and Genotype-Phenotype Correlations in Inherited Kidney Diseases.Life (Basel, Switzerland) · 2026Article
- HeterozygousiScience · 2026Article
239 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Knowledge of protein structure can be used to predict the phenotypic consequence of a missense variant. Since structural coverage of the human proteome can be roughly tripled to over 50% of the residues if homology-predicted structures are included in addition to experimentally determined coordinates, it is important to assess the reliability of using predicted models when analyzing missense variants. Accordingly, we assess whether a missense variant is structurally damaging by using experimental and predicted structures. We considered 606 experimental structures and show that 40% of the 1965 disease-associated missense variants analyzed have a structurally damaging change in the mutant structure. Only 11% of the 2134 neutral variants are structurally damaging. Importantly, similar results are obtained when 1052 structures predicted using Phyre2 algorithm were used, even when the model shares low (<40%) sequence identity to the template. Thus, structure-based analysis of the effects of missense variants can be effectively applied to homology models. Our in-house pipeline, Missense3D, for structurally assessing missense variants was made available at http://www.sbg.bio.ic.ac.uk/~missense3d.
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.