I have found a novel mutation in clotting factor 2 gene in an exon (midway through the exon), however, on checking with mutation tester it is showing that the mutation may result in splice site changes. I am unable to understand the same. What other prediction softwares can I use (other than Polyphen2, SIFT) to confirm the effect of the mutation on protein function.
Some of the software's
http://mutationassessor.org/r3/
http://cadd.gs.washington.edu/
Mutation taster only just the assumption. If it is in the middle than its not a splice site.
If its a missense than kindly look in the ExAc and 100 genomes. if its present than its not a mutation.
Thank you
Indeed, the mutation in the exon can reveal a splice site. This new site will produce a frameshift in the messenger and change the sequence of the protein .
The mutation may also affect the binding site of proteins involved in the splice (ESE or ISE sites)
You can test the effect on splicing with Human splicing finder (http://www.umd.be/HSF/)
Best regards
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