ArticleNucleic acids research2016
PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 58 citations in OpenAlex.
- Mosaic variants of neurodevelopmental and mitochondrial genes in postmortem paraventricular thalamus in bipolar disorder detected by deep exome sequencing.Psychiatry and clinical neurosciences · 2025Article
- Single-molecule DNA analysis implicates brain mitochondria pathology in bipolar disorder.Molecular psychiatry · 2025Article
- Characterization and comparative analysis of the complete mitochondrial genome of Phlomoides rotata, a traditional Tibetan medicinal plant.BMC genomics · 2025Article
- Mitochondrial DNA variant detection in over 6,500 rare disease families by the systematic analysis of exome and genome sequencing data resolves undiagnosed cases.HGG advances · 2025Article
- Analysis of mutations in mitochondrial transfer RNA genes and the maternal inheritance of polycystic ovary syndrome.Frontiers in endocrinology · 2025Article
- 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
- Mitochondrial and Nuclear DNA Variants in Amyotrophic Lateral Sclerosis: Enrichment in the Mitochondrial Control Region and Sirtuin Pathway Genes in Spinal Cord Tissue.Biomolecules · 2024Article
- Deep exome sequencing identifies enrichment of deleterious mosaic variants in neurodevelopmental disorder genes and mitochondrial tRNA regions in bipolar disorder.Molecular psychiatry · 2023Article
- The mutational analysis of mitochondrial DNA in maternal inheritance of polycystic ovarian syndrome.Frontiers in endocrinology · 2023Article
- Individual Genetic Heterogeneity.Genes · 2022Review
- Mitochondrial DNA variation across 56,434 individuals in gnomAD.Genome research · 2022Article
- Genetic Alterations in Mitochondrial DNA Are Complementary to Nuclear DNA Mutations in Pheochromocytomas.Cancers · 2022Article
- PON-All: Amino Acid Substitution Tolerance Predictor for All Organisms.Frontiers in molecular biosciences · 2022Article
- Accelerated expansion of pathogenic mitochondrial DNA heteroplasmies in Huntington's disease.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Systematics for types and effects of RNA variations.RNA biology · 2021Article
- Whole mitochondrial genome analysis in Chinese patients with keratoconus.Molecular vision · 2021Article
- Possible A2E Mutagenic Effects on RPE Mitochondrial DNA from Innovative RNA-Seq Bioinformatics Pipeline.Antioxidants (Basel, Switzerland) · 2020Article
- Clinical Bioinformatics in Precise Diagnosis of Mitochondrial Disease.Clinics in laboratory medicine · 2020Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transfer RNAs (tRNAs) are essential for encoding the transcribed genetic information from DNA into proteins. Variations in the human tRNAs are involved in diverse clinical phenotypes. Interestingly, all pathogenic variations in tRNAs are located in mitochondrial tRNAs (mt-tRNAs). Therefore, it is crucial to identify pathogenic variations in mt-tRNAs for disease diagnosis and proper treatment. We collected mt-tRNA variations using a classification based on evidence from several sources and used the data to develop a multifactorial probability-based prediction method, PON-mt-tRNA, for classification of mt-tRNA single nucleotide substitutions. We integrated a machine learning-based predictor and an evidence-based likelihood ratio for pathogenicity using evidence of segregation, biochemistry and histochemistry to predict the posterior probability of pathogenicity of variants. The accuracy and Matthews correlation coefficient (MCC) of PON-mt-tRNA are 1.00 and 0.99, respectively. In the absence of evidence from segregation, biochemistry and histochemistry, PON-mt-tRNA classifies variations based on the machine learning method with an accuracy and MCC of 0.69 and 0.39, respectively. We classified all possible single nucleotide substitutions in all human mt-tRNAs using PON-mt-tRNA. The variations in the loops are more often tolerated compared to the variations in stems. The anticodon loop contains comparatively more predicted pathogenic variations than the other loops. PON-mt-tRNA is available at http://structure.bmc.lu.se/PON-mt-tRNA/.
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