I am currently looking at a bunch of SNPs from a genome wide association study. Couple of these SNPs are non-synonymous and present in the coding region. For example, in case of a particular SNP, we noticed that the gene codes for different transcripts and the SNP is present only in 5 out of total of 10 transcript including the longest transcript.
From a biological view point, what will be the functional implication / functional effect of such SNP which may or may not express in the protein product due to alternate splicing ?
While discussing the results, is it alright to explain the results using the longest transcript ?
What will be the best way to assess the effect of such a SNP, given that the gene with that particular encodes multiple transcript due alternate exons and overlapping splice sites ?
Is there any tool which can predict functional effect of such SNPs ?
Looking forward your thoughtful insights. Thanks in advance.
PolyPhen installation steps didn't proceeded beyond the makeblastdb was running for 2 days and still no sign of completing the process of formatting. Finally I got the results via the web interface using rs numbers.
Thanks for the note on Polyphen. I am still at the step 7 of PPH2 installation, makeblastdb terminated in between and I' am running it again. I hope the server will be up by tomorrow, if my installation fails, I will try at the Polyphen server.
ok Khader, thanks for telling me