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Defining LoF mutations with Annovar

I have annovar gene and exon annotations for SNVs and I would like to get the Loss of Function (LoF) alleles from this list.

Using the annovar annotations are these considered to be LoF?

  • frameshift (insertion/deletion)
  • stopgain
  • stoploss
  • splicing (?)

Any input is appreciated :)

snv annovar
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updated by mforde84 mforde84 • written by QVINTVS_FABIVS_MAXIMVS QVINTVS_FABIVS_MAXIMVS

1 answer

You'd have to look at the protein to really be sure. The first three are probable, especially if they are early on in the coding sequence (e.g., exon 1 / 2). Splicing might be LOF, GOF, both, benign. For example, say a silenced oncodriver is spliced into an actively transcribed oncosuppressor and in such a way that disrupts the suppressor.

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written by mforde84 mforde84

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