Question: functional assessment of synonymous SNPs
1
gravatar for 12021560-002
3.4 years ago by
12021560-00210
12021560-00210 wrote:

Hi I have a question. I have a gene list and variants associated with these genes and want to carry out the functional assessment of those variants although I have found some tools for nonsynonymous variants like SIFT,POLYPHEN etc. but I have not found any tool for functional assessment of synonymous variants. Could you please suggest name of some tools for synonymous variants which help me to get functional insight of these variants based on certain parameters like a threshold or score???

ADD COMMENTlink modified 3.4 years ago by Garan580 • written 3.4 years ago by 12021560-00210
3
gravatar for Denise - Open Targets
3.4 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

Use the Variant Effect Predictor and select the LoFtool, available both in the online interface and Perl script as a VEP plugin. LoFtool gives you 'a rank of genic intolerance and consequent susceptibility to disease based on the ratio of Loss-of-function (LoF) to synonymous mutations for each gene in 60,706 individuals from ExAC).

ADD COMMENTlink written 3.4 years ago by Denise - Open Targets5.0k
1
gravatar for RamRS
3.4 years ago by
RamRS24k
Houston, TX
RamRS24k wrote:

Synonymous variants are not significant at the protein level - you should look at DNA/RNA level effects. Look for motifs affected, binding sites disrupted, cryptic splice sites created, etc.

Tools should not the first thing on your list - the concept of consequence/effect should. Your biological question will drive the kind of effects relevant to your analysis, and the kind of effect you're looking for will determine what tool would be appropriate.

ADD COMMENTlink written 3.4 years ago by RamRS24k
1

The VEP also tells whether the variant falls in a regulatory motif or not. Use the --regulatory flag with the script version, or check if the 'Get the regulatory region consequence' is selected under Extra options in the online version.

ADD REPLYlink written 3.4 years ago by Denise - Open Targets5.0k
1

I did not know of this option in VEP - thank you so much!

ADD REPLYlink written 3.4 years ago by RamRS24k

Tools should not the first thing on your list - the concept of consequence/effect should.

Truth!

ADD REPLYlink written 3.4 years ago by John12k
1
gravatar for Garan
3.4 years ago by
Garan580
United Kingdom
Garan580 wrote:

You could also try something like SilVA

http://compbio.cs.toronto.edu/silva/

Identification of deleterious synonymous variants in human genomes.

ADD COMMENTlink written 3.4 years ago by Garan580
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