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Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP

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  • Sanjay Sonney
  • Jeremy Leipzig
  • Marie T Lott
  • Shiping Zhang
  • Vincent Procaccio
  • Douglas C Wallace
  • Neal Sondheimer

Abstract

Novel or rare variants in mitochondrial tRNA sequences may be observed after mitochondrial DNA analysis. Determining whether these variants are pathogenic is critical, but confirmation of the effect of a variant on mitochondrial function can be challenging. We have used available databases of benign and pathogenic variants, alignment between diverse tRNAs, structural information and comparative genomics to predict the impact of all possible single-base variants and deletions. The Mitochondrial tRNA Informatics Predictor (MitoTIP) is available through MITOMAP at www.mitomap.org. The source code for MitoTIP is available at www.github.com/sonneysa/MitoTIP.

Suggested Citation

  • Sanjay Sonney & Jeremy Leipzig & Marie T Lott & Shiping Zhang & Vincent Procaccio & Douglas C Wallace & Neal Sondheimer, 2017. "Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP," PLOS Computational Biology, Public Library of Science, vol. 13(12), pages 1-8, December.
    • Handle: RePEc:plo:pcbi00:1005867
    DOI: 10.1371/journal.pcbi.1005867
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    Cited by:

    1. Yiqin Wang & Xiaoxian Guo & Xiumei Hong & Guoying Wang & Colleen Pearson & Barry Zuckerman & Andrew G. Clark & Kimberly O. O’Brien & Xiaobin Wang & Zhenglong Gu, 2022. "Association of mitochondrial DNA content, heteroplasmies and inter-generational transmission with autism," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Ieva Keraite & Philipp Becker & Davide Canevazzi & Cristina Frias-López & Marc Dabad & Raúl Tonda-Hernandez & Ida Paramonov & Matthew John Ingham & Isabelle Brun-Heath & Jordi Leno & Anna Abulí & Elen, 2022. "A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Salvatore Daniele Bianco & Luca Parca & Francesco Petrizzelli & Tommaso Biagini & Agnese Giovannetti & Niccolò Liorni & Alessandro Napoli & Massimo Carella & Vincent Procaccio & Marie T. Lott & Shipin, 2023. "APOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Joke Mertens & Florence Belva & Aafke P. A. van Montfoort & Marius Regin & Filippo Zambelli & Sara Seneca & Edouard Couvreu de Deckersberg & Maryse Bonduelle & Herman Tournaye & Katrien Stouffs & Kurt, 2024. "Children born after assisted reproduction more commonly carry a mitochondrial genotype associating with low birthweight," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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