About the Rescue Stop Site

The disruption of stop codons has been found to cause disease, but the interpretation of possible consequences of such disruptions is often difficult.One way of identifying the potential deleteriousness of a disrupted stop codon is to determine the extent to which the CDS has been extended, and the 3’UTR expunged.
The effects of ntroducing additional amino acids may vary between transcripts, however, some key outcomes include protein misfolding and the potential for changes in phobicity of the protein product
The 3’ UTR of a given gene includes important regulatory elements, including polyA sies and signals, downstream open reading frames (dORFs), and RNA binding protein binding sites. When these elements are disrupted it has been shown to lead to disease phenotypes.
The Rescue Stop Site provides the location of the next available in-frame stop codon, and both the extension of CDS that would be created if it were to be used, and the proportion of 3’ UTR that would be lost. This is currently limited to Ensembl transcripts (release 110). Read more about the role of 3' UTRs, regulatory variants in disease, and the consequences of stop loss in the following papers:
1 : Ellingford et al, Recommendations for clinical interpretation of variants found in non-coding regions of the genome , Genome Medicine (2023).
2 : Martin-Geary et al, Systematic identification of disease-causing promoter and untranslated region variants in 8,040 undiagnosed individuals with rare disease , medRxiv (2023).
3 : Bauer et al (2023), Loss of function SMAD4 nonstop mutations in human cancer , Histopathology (2023).

About the Team

The Rescue Stop Site was developed by the Computational Rare Disease Genomics Lab (CRDG). CRDG specialises in identifying the role of non-protein-coding variants in rare genetic diseases through the use of bioinformatics on large exome and genome sequencing datasets. We are based out of the Big Data Institute at the University of Oxford. You can learn more about our lab at our website .

Tools and Data

The Rescue Stop Site was built using R version 4.3.1 (2023-06-16), R studio version 2023.09.0+463, and the packages ‘base’, ‘utils’, ‘ggplot2’, ’shiny’, 'shinyjs', ’shinytheme’, ’stats’, ’dplyr’, ’tidyr’, ’stringr’, ’beepr’ and ‘Biostrings’. Stop codon and sequence data was collected using the ‘biomaRt’ R package and Ensembl release 110. This was further supplemented using polyadenylation data from PolyA DB , alongside MANE transcript data, and LOEUF scores.
All code and data is available through our GitHub repo <insert here> If you face any issues or wish to report a bug whilst using the Rescue Stop Site please get in touch with us by opening up an issue in our repository's GitHub repo

Acknowledgements

This work was funded through Wellcome Trust and the Royal Society (Sir Henry Dale Fellowship awarded to Nicola Whiffin; 220134/Z/20/Z) and the Rosetrees Trust (H5R01320). The ShinyTheme "lumen" was used for generating the template for this application. Our DNA Logo icon was created by Freepik - Flaticon. All rights reserved for their respective owners.

How to use the Rescue Stop Site

*BETA PHASE*

the STOP g.APP is currently open for beta testing while we implement some additional features. We would appreciate any and all feedback, comments or suggestions you may have during this time!

Variant queries

Variants should be input in the format chr[N]:[POSITION]_REF/ALT, i.e. chr19:45163192_T/C or 19:45163192_T/CGG. For single nucleotide polymorphisms the STOP gAPP can identify if the variant would disrupt, or preserve (i.e. result in an alternate stop motif) the stop codon. For multi nucleotide variants, alternate stops are calculated with reference to the frame change (if any) resulting from a frameshift due to the variant.

Gene level queries

At a gene level, the STOP gAPP will take in a gene symbol, and show the next in-frame stop downstream from the canonical stop for each transcript associated with that gene. Simply input a gene symbol i.e. MEF2c, TGFB1, tp53, and select a transcript of interest from the drop down menu.

Transcript specific queries

For queries relating to a particular transcript, type or paste the Ensembl transcript I.D of the transcript of interest into the box, and the next in-frame stop will be shown.

The visualisation tab

The visualisation tab will give you an overview of the impact of a stop-loss variant, including an illustration of the wild-type CDS length, and any additions to the CDS that would occur as a result of a downstream stop being used

The consequence information tab

The consequence information tab provides a table view of the impact of a stop-loss variant. This includes general information about the transcript in question, alongside specific information about the predicted stop, including the downstream stop motif, genomic coordinates, and extension statistics.