Question: Annotating a variant's effect: frameshift or nonsense?
1
gravatar for alex.rubinsteyn
4.2 years ago by
United States
alex.rubinsteyn130 wrote:

I'm looking at a mutation which, due to a frameshift, immediately introduces a stop codon. When describing the effect of this mutation would you call it a "frameshift", a "nonsense" mutation, or some hybrid of the two?

 

More broadly, I'm trying to figure out the right terminology for talking about protein-level variant effects but finding the basic terms seem to sometimes overlap. A frameshift can, in effect cause the premature insertion of a stop codon, or the substitution of the tail of a coding sequence with some other sequence. How do we differentiate these two cases?

annotation effect variant • 1.6k views
ADD COMMENTlink modified 4.2 years ago by Pierre Lindenbaum119k • written 4.2 years ago by alex.rubinsteyn130
2
gravatar for Pierre Lindenbaum
4.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

frameshift_truncation http://www.sequenceontology.org/miso/current_svn/term/SO:0001910

"A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature."

ADD COMMENTlink written 4.2 years ago by Pierre Lindenbaum119k
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