Impact of missense snps in the fuction or structure of proteins

Question

[gcarvalho]

Hello everybody, I having used some software to analyze the impact of missense SNPs in the function and structure of some proteins (polyphen2, multipred, mutation assessor, SNP&GO, SNAP). It came a doubt, researched in some places and I didn't found anything like that yet, as these software analyze SNPs individually, anyone knows any software/algorithm to analyze sets of SNPs that when together cause a high impact than individually or with other different SNPs?

[Sean Davis]

Are you referring to several snps in the same sample occurring simultaneously? If so, how often do you see that? And how often, when you do see it, would you expect that the combination might be worse than a single deleterious variant? Do you have phasing on your variants?

[gcarvalho]

Yeah, like I said I have not seen anything like it, thought about it because in protein modeling we can see as a set of missense SNPs impact the structure of a protein. For example, it's possible to know whether the set with SNPs 1, 2 and 3 has a high functional impact on the structure of the protein than the set with SNPs 2 and 3, occurring simultaneously.

Thank you for your interest Mr. Sean

[Sean Davis]

I don't know of a software that does what you are asking, but I would suspect that such cases are very rare events.

Answer 1

[cpad0112]

Are you looking for a tool that assigns a significance (some thing like clinically relevant) score for each SNP in it's context (transcript, disease, tissue etc) and then summing them up (statistically or whatsoever) to arrive at a sum effect of SNVs in gene/locus/region? I haven't come across one so far.

[gcarvalho]

Nop, it's like Mr Sean told. In the same sample we searching for the most impactful set of missense SNPs comparing among them, like my example.

Thank you for your interest :D