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  • 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

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

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    • #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.

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      • #4
        awesome! Many thanks to both of you.

        Happy Holiday~

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        • #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?

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          • #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

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            • #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".

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

                This documentation lists them

                http://www.ensembl.org/info/docs/variation/index.html

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

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                • #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

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                  • #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

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

                      You can browse their resource here

                      http://www.sequenceontology.org/cgi-bin/miso.cgi

                      stop lost seems to be their term for this

                      http://www.sequenceontology.org/miso...erm/SO:0001578

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                      • #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

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                        • #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.

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                          • #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

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                            • #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?

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