Latest updates
Releases, publications and announcements from the MitImpact team.
MitImpact 4 is published in Nucleic Acids Research. MitImpact 4: a genome-wide resource for the interpretation of coding and non-coding mitochondrial DNA variants [link]. If you use MitImpact, please cite this paper (see How to cite).
MitImpact 4 is here. This release takes MitImpact beyond missense variants: it covers tRNA and rRNA variants (nAPOGEE) alongside APOGEE2's five classes for protein-coding ones. Source annotations were refreshed throughout. The interface is new as well, with interactive statistics for each molecule class and a VCF annotator.
nAPOGEE v1.0.0 released, now available for download from the top-right menu. This release includes pathogenicity scores and probabilities for all mitochondrial noncoding variants. VUS are subclassified into cold (VUS−), actual (VUS), and hot (VUS+) variants. We also published the preprint entitled nAPOGEE: A machine-learning platform for clinically actionable pathogenicity assessment of all mitochondrial noncoding variants [link].
MitImpact 3D 3.1.3 released, with minor fixes in the search engine and VCF annotator. Updated MITOMAP, ClinVar, and dbSNP. Added OMIM and HGNC ids and HGVS-based variant descriptions to aid diagnostic reporting. Added AlphaMissense predictions and ToMMo 54KJPN allele frequencies (see the Output legend).
We announce the alpha release of APOGEE pathogenicity prediction scores for tRNA variants. A bulk download of all possible tRNA variants is available; each carries a pathogenicity score (0 = benign, 1 = pathogenic) and an out-of-bag unbiased score we recommend. Send us your feedback!
A paper entitled APOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants was published in Nature Communications and is available here.
MitImpact 3D 3.1.2 released, with minor fixes of HelixMTdb frequency values, MITOMAP updated (July 1st), and intra-VUS soft thresholds introduced.
MitImpact 3D 3.1.1 released, with minor fixes to the conservation scores, SIFT4G added, and APOGEE1 reintroduced for backward compatibility.
A preprint entitled APOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants was posted [link].
MitImpact 3D 3.1.0 released. It contains the new APOGEE 2 scores, hazards, and five pathogenicity classes. MitImpact and APOGEE are freely available for non-commercial purposes, check the license.
MitImpact 3D 3.0.8 released, with minor fixes on pathogenicity thresholds and the update of ClinVar and MITOMAP (July 2022). Added HelixMTdb annotations.
MitImpact 3D 3.0.7 released, with fixes to the search engine and updates to ClinVar (Oct 2021), dbSNP (v155), gnomAD (v3.1) and MITOMAP.
Nucleic Acids Research published our paper MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits [link].
MitImpact 3D 3.0.6 released, with fixes to the flat-file database, tooltips to help interpret scores in the result page, and two tutorial-like case studies.
Added the ability to directly search for a variant and show its information, also exposed through a RESTful API.
MitImpact 3D 3.0.5 released! Minor fixes and updates to frequency and phenotype databases (dbSNP 152, ClinVar March 2020, COSMIC 90, MITOMAP February 2020).
MitImpact 3D 3.0.2 released! Molecular dynamics added for selected mutations.
MitImpact 3D released! A revamped results page with more info and visualizations, plus Compensated Pathogenic Deviations (CPD), ΔΔG energy changes, InterP/IntraP covariation analysis, and EVmutation score.
PLoS Comput Biol. published our paper: High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE [link].
MitImpact 2.7 released! New annotations and bug fixes.
MitImpact 2.5 released!
Methods Mol Biol. published our chapter: A Broad Overview of Computational Methods for Predicting the Pathophysiological Effects of Non-synonymous Variants [link].
MitImpact 2.4 released! Several new annotations available.
Improved programmatic access to data through the new RESTful interface.
Human Mutation published our paper: MitImpact: an exhaustive collection of pre-computed pathogenicity predictions of human mitochondrial non-synonymous variants [link].
MitImpact 1.0 launch! MitImpact annotates all possible mutations in the 13 mitochondrial proteins by 5 missense pathogenicity predictors, 2 consensus aggregators, and 5 sources of functional evidence.