Back to Search
Start Over
Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel
- Source :
- PLoS Computational Biology, Vol 16, Iss 4, p e1007749 (2020), PLoS Computational Biology
- Publication Year :
- 2020
- Publisher :
- Public Library of Science (PLoS), 2020.
-
Abstract
- The renal outer medullary potassium (ROMK) channel is essential for potassium transport in the kidney, and its dysfunction is associated with a salt-wasting disorder known as Bartter syndrome. Despite its physiological significance, we lack a mechanistic understanding of the molecular defects in ROMK underlying most Bartter syndrome-associated mutations. To this end, we employed a ROMK-dependent yeast growth assay and tested single amino acid variants selected by a series of computational tools representative of different approaches to predict each variants’ pathogenicity. In one approach, we used in silico saturation mutagenesis, i.e. the scanning of all possible single amino acid substitutions at all sequence positions to estimate their impact on function, and then employed a new machine learning classifier known as Rhapsody. We also used two additional tools, EVmutation and Polyphen-2, which permitted us to make consensus predictions on the pathogenicity of single amino acid variants in ROMK. Experimental tests performed for selected mutants in different classes validated the vast majority of our predictions and provided insights into variants implicated in ROMK dysfunction. On a broader scope, our analysis suggests that consolidation of data from complementary computational approaches provides an improved and facile method to predict the severity of an amino acid substitution and may help accelerate the identification of disease-causing mutations in any protein.<br />Author summary As the number of sequenced human genomes rises, a major challenge is to identify which single amino acid variations in a protein affect function and predispose individuals to disease. While predictive algorithms are available for this purpose, a comparative analysis of recently developed algorithms has not been adequately performed, nor is it clear whether combining algorithms would improve predictive power. To this end, we compared the efficacy of three publicly available algorithms and applied the results to Bartter syndrome, a human disease for which numerous poorly-characterized single amino acid variants have been identified and for which there is no cure. In silico saturation mutagenesis, i.e., the computational prediction of pathogenesis for every possible amino acid substitution, allowed us to experimentally test predictions by measuring the activity of an ion channel linked to Bartter syndrome. Based on data from blinded experiments, we discovered that Rhapsody and EVmutation successfully predicted deleterious mutations. Moreover, Rhapsody—which takes into account evolutionary as well as structural and dynamic considerations—predicted that >90% of known Bartter syndrome mutations are deleterious. Overall, our data will aid investigators who wish to test single amino acid variants in any protein and aid biomedical researchers who wish to develop hypotheses on the potential severity of genetic variants uncovered from genome databases.
- Subjects :
- 0301 basic medicine
Potassium Channels
Physiology
Gene Identification and Analysis
Pathogenesis
Kidney
Pathology and Laboratory Medicine
medicine.disease_cause
Biochemistry
Ion Channels
Database and Informatics Methods
0302 clinical medicine
Medicine and Health Sciences
Missense mutation
Amino Acids
Biology (General)
Mutation
Ecology
Organic Compounds
Physics
Electrophysiology
Chemistry
Deletion Mutation
Computational Theory and Mathematics
Modeling and Simulation
Physical Sciences
Research Article
Substitution Mutation
QH301-705.5
In silico
Mutation, Missense
Biophysics
Neurophysiology
Saccharomyces cerevisiae
Computational biology
Biology
Research and Analysis Methods
Bartter syndrome
03 medical and health sciences
Cellular and Molecular Neuroscience
Genetics
medicine
Humans
Potassium Channels, Inwardly Rectifying
Saturated mutagenesis
Mutation Detection
Molecular Biology
Ecology, Evolution, Behavior and Systematics
Point mutation
Organic Chemistry
Chemical Compounds
Bartter Syndrome
Computational Biology
Biology and Life Sciences
Proteins
Kidney metabolism
medicine.disease
Biological Databases
030104 developmental biology
Amino Acid Substitution
Mutagenesis
Mutation Databases
Potassium
ROMK
030217 neurology & neurosurgery
Neuroscience
Subjects
Details
- Language :
- English
- ISSN :
- 15537358
- Volume :
- 16
- Issue :
- 4
- Database :
- OpenAIRE
- Journal :
- PLoS Computational Biology
- Accession number :
- edsair.doi.dedup.....0c6b12b10302ce3c65199ee5ed39a8c4