Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • yuanzhi
    Member
    • Aug 2010
    • 19

    how to define nonsense mutation

    From several genetics books I have read, nonsense mutations change a codon for an amino acid to a stop codon.

    then how to define a mutation change a stop codon to a codon for an amino acid? still nonsense mutation?

    Thanks
  • bpetersen
    Member
    • Mar 2010
    • 20

    #2
    I think you're looking for the term "readthrough mutation".
    Have a nice day!

    Comment

    • Jon_Keats
      Senior Member
      • Mar 2010
      • 279

      #3
      Not a nonsense change for sure as that exclusively means the creation of a stop codon.

      These changes that eliminate the proper stop codon and allow translation to continue on into the 3'UTR finally have an official nomenclature (http://www.hgvs.org/mutnomen/recs-prot.html) of "NO-STOP" changes. Though others (http://www.sanger.ac.uk/perl/genetic...ummary&id=5333) use "non-stop extension" which seems a bit more descriptive and I've also see them listed as "missense-stopcodon".

      This is definately one of two special mutation classes, that being mutations of the initiating methionine and stop codon.

      Comment

      • yuanzhi
        Member
        • Aug 2010
        • 19

        #4
        awesome! Many thanks to both of you.

        Happy Holiday~

        Comment

        • yuanzhi
          Member
          • Aug 2010
          • 19

          #5
          I just thought of another question. Can we call this readthrough mutation or non-stop extension as nonsynonymous mutation? Or, nonsynonymous mutation includes missense and nonsense?

          Comment

          • ntremblay
            Member
            • Dec 2009
            • 31

            #6
            I would say it is a non-synonymous mutation as it cause a change in the translated amino acid sequence ...!
            Nicolas Tremblay
            Graduate Student

            Cardiovascular Genetics - Andelfinger Lab
            CHU Ste-Justine Research Center

            Comment

            • mard
              Member
              • Jan 2010
              • 21

              #7
              Originally posted by yuanzhi View Post
              From several genetics books I have read, nonsense mutations change a codon for an amino acid to a stop codon.

              then how to define a mutation change a stop codon to a codon for an amino acid? still nonsense mutation?

              Thanks
              Just to let you know Ensembl class those mutations as "Stop lost".

              Comment

              • laura
                Senior Member
                • Sep 2008
                • 151

                #8
                The ensembl database is a good place to look for what the different sort of consequences

                This documentation lists them



                For a consequence which is non synonymous it means the base change results in an amino acid change in the protein sequence

                Comment

                • bioinfosm
                  Senior Member
                  • Jan 2008
                  • 483

                  #9
                  'Read through' are what they are called then!

                  We also recently saw quite a few 'loss of stop codon' mutations in exome data.. and was not sure how to interpret/annotate/log them
                  --
                  bioinfosm

                  Comment

                  • Jon_Keats
                    Senior Member
                    • Mar 2010
                    • 279

                    #10
                    Originally posted by bioinfosm View Post
                    'Read through' are what they are called then!

                    We also recently saw quite a few 'loss of stop codon' mutations in exome data.. and was not sure how to interpret/annotate/log them
                    This thread shows a common problem of lack of international standards and referencing. Last time I checked hgvs (www.hgvs.org) is a standards group that most follow or should follow. What you, your facility, your boss thinks is correct or even others follow is not a standard that deserves an exclamation mark in a public form!!

                    Thus "No-Stop"
                    Last edited by Jon_Keats; 12-01-2010, 11:26 AM. Reason: Fixed URL error noted by other participant

                    Comment

                    • laura
                      Senior Member
                      • Sep 2008
                      • 151

                      #11
                      The Sequence Ontology group are defining a standard ontology for variant consequences

                      You can browse their resource here



                      stop lost seems to be their term for this

                      Comment

                      • bioinfosm
                        Senior Member
                        • Jan 2008
                        • 483

                        #12
                        2 standards already then = "No-Stop" and "Stop lost"

                        I think the key is, enforce a standard locally, but be aware of the synonyms, because bioinformatics standardization is not present yet
                        --
                        bioinfosm

                        Comment

                        • Jon_Keats
                          Senior Member
                          • Mar 2010
                          • 279

                          #13
                          Agreed, hopefully there can be a clear winner in the very near future. This thread started with a very junior question that has a definite unequivocal answer, as the definition of a nonsense change is well established and an accepted nomenclature for the type of event. Hopefully a standard can be reached soon, as the number of genome papers and data sharing will only increase and standardized nomenclature will becomes ever so important.

                          Comment

                          • laura
                            Senior Member
                            • Sep 2008
                            • 151

                            #14
                            The Sequence Ontology consortium being the people who define ontologies in genomics/bioinformatics are trying to solve this problem by providing a standard ontology and being open to suggestions about additions or changes

                            Ensembl is certainly adopting the SO consequence ontology so lets hope others follow suit

                            Comment

                            • Joann
                              Senior Member
                              • Oct 2008
                              • 230

                              #15
                              harmonization

                              Nomenclature groups should strive for harmonization and cite the earliest published convention assembled by an authoritative group--for use in naming an identical concept/event, that is. Nuances and hierarchical relationships should be explored and articulated as part of gaining consensus. There is nothing like using exactly the right word in annotating sequence data, no?

                              Comment

                              Latest Articles

                              Collapse

                              • seqadmin
                                Pathogen Surveillance with Advanced Genomic Tools
                                by seqadmin




                                The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
                                03-24-2025, 11:48 AM
                              • seqadmin
                                New Genomics Tools and Methods Shared at AGBT 2025
                                by seqadmin


                                This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

                                The Headliner
                                The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
                                03-03-2025, 01:39 PM

                              ad_right_rmr

                              Collapse

                              News

                              Collapse

                              Topics Statistics Last Post
                              Started by seqadmin, 03-20-2025, 05:03 AM
                              0 responses
                              49 views
                              0 reactions
                              Last Post seqadmin  
                              Started by seqadmin, 03-19-2025, 07:27 AM
                              0 responses
                              57 views
                              0 reactions
                              Last Post seqadmin  
                              Started by seqadmin, 03-18-2025, 12:50 PM
                              0 responses
                              50 views
                              0 reactions
                              Last Post seqadmin  
                              Started by seqadmin, 03-03-2025, 01:15 PM
                              0 responses
                              200 views
                              0 reactions
                              Last Post seqadmin  
                              Working...