ReviewGenome medicine2017
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.
Review in Genome medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 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
40 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Variant effect predictors: a systematic review and practical guide.Human genetics · 2024Pooled it
- Host genotype and sex shape influenza evolution and defective viral genomes.Nature communications · 2026Article
- Cancer-associated TRF1 mutations alter PARP1 interaction dynamics: an in silico study.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Translating pharmacogenomic sequencing data into drug response predictions-How to interpret variants of unknown significance.British journal of clinical pharmacology · 2025Review
- Structural and Dynamic Analyses of Pathogenic Variants inLife (Basel, Switzerland) · 2024Article
- Cellular and epigenetic perspective of protein stability and its implications in the biological system.Epigenomics · 2024Review
- SLC6A1 variant pathogenicity, molecular function and phenotype: a genetic and clinical analysis.Brain : a journal of neurology · 2023Article
- 3DVizSNP: a tool for rapidly visualizing missense mutations identified in high throughput experiments in iCn3D.BMC bioinformatics · 2023Article
- Unravelling the epidemiological diversity of Zika virus by analyzing key protein variations.Archives of virology · 2023Article
- VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses.Molecular biology and evolution · 2022Article
- Identifying intragenic functional modules of genomic variations associated with cancer phenotypes by learning representation of association networks.BMC medical genomics · 2022Article
- Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure.Nature communications · 2022Article
- Calculating genetic risk for dysfunction in pleiotropic biological processes using whole exome sequencing data.Journal of neurodevelopmental disorders · 2022Article
- Comprehensive analysis of 1R- and 2R-MYBs reveals novel genic and protein features, complex organisation, selective expansion and insights into evolutionary tendencies.Functional & integrative genomics · 2022Article
- SWAAT Bioinformatics Workflow for Protein Structure-Based Annotation of ADME Gene Variants.Journal of personalized medicine · 2022Article
- In-silico phenotype prediction by normal mode variant analysis in TUBB4A-related disease.Scientific reports · 2022Article
- Interpreting the spectrum of gamma-secretase complex missense variation in the context of hidradenitis suppurativa-AnFrontiers in genetics · 2022Article
- Pathogenic variation types in human genes relate to diseases through Pfam and InterPro mapping.Frontiers in molecular biosciences · 2022Article
- Computational study of the impact of nucleotide variations on highly conserved proteins: In the case of actin.Biophysics and physicobiology · 2022Article
- Linking genome variants to disease: scalable approaches to test the functional impact of human mutations.Human molecular genetics · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
37 authors.
Funding
Abstract
The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods.
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.