Question: Defining LoF mutations with Annovar
1
gravatar for QVINTVS_FABIVS_MAXIMVS
2.5 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.3k wrote:

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 • 936 views
ADD COMMENTlink modified 2.5 years ago by mforde841.2k • written 2.5 years ago by QVINTVS_FABIVS_MAXIMVS2.3k
1
gravatar for mforde84
2.5 years ago by
mforde841.2k
mforde841.2k wrote:

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.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by mforde841.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1310 users visited in the last hour