[ Start MTR Gene Viewer ]


Traynelis J.,* Silk M.,* Wang Q., Berkovic S.F., Liu L., Ascher D.B., Balding D.J., Petrovski S. (2017). Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation. Genome Research (2017)


What is the Missense Tolerance Ratio?

The MTR aims to quantify the amount of purifying selection acting specifically on missense variants in a given window of protein-coding sequence. It is estimated across sliding windows of 31 codons (default) and uses observed standing variation data from the WES component of the Exome Aggregation Consortium Database (ExAC), version 2.0 (http://gnomad.broadinstitute.org)


Exome-wide evaluation of MTR utility using ClinVar Pathogenic variants and novel control missense variants that did not contribute to score construction. See Legend for further details. Source data available upon request slavep@unimelb.edu.au.
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How to use the MTR Gene Viewer

HGNC symbols resolve to a canonical-defined transcript, as defined by Ve!P. If one is not defined, then the longest protein-coding sequence transcript with a valid CCDS in Ensembl v75 is selected. Alternatively, users can directly enter a Ensembl ENST (v75) transcript.

Each window’s MTR estimate is supplemented with a study-wide false discovery rate adjusted binomial exact test for deviation from MTR=1 (where the standing variation observed proportion equals the expected proportion of missense variants). Red MTR regions denote windows achieving a FDR < 0.10.



     

Gaps in MTR plots align with windows where the total observed standing variation < 3; commonly reflecting inadequate sequencing coverage in the standing variation sample.

   

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CHANGELOG

v0.1

v0.2

v0.3