Aenmd: Annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants.

ABSTRACT: DNA changes that cause premature termination codons (PTCs) represent a large fraction of clinically relevant pathogenic genomic variation. Typically, PTCs induce a transcript's degradation by nonsense-mediated mRNA decay (NMD) and render such changes loss-of-function alleles. However, certain PTC-containing transcripts escape NMD and can exert dominant-negative or gain-of-function (DN/GOF) effects. Therefore, systematic identification of human PTC-causing variants and their susceptibility to NMD contributes to the investigation of the role of DN/GOF alleles in human disease. Here we present aenmd, a software for annotating PTC-containing transcript-variant pairs for predicted escape from NMD. aenmd is user-friendly and self-contained. It offers functionality not currently available in othe

SUBMITTER: Klonowski J 

PROVIDER: S-EPMC10055276 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature