I'm fairly new to studying genetics but want to understand SNPs better. When a SNP is found in an exon, is it assumed to change the amino acid sequence or assumed not to change it? Or is there no pattern, and each case requires individual analysis? It would seem to me that SNPs that change the amino acid sequence would have to be more rare.
Please see the discussion regarding question 4835 as Alex suggests. And make no assumptions! For a long time, many thought that synonymous SNPs were not interesting, but that is changing. You asked specifically about SNPs in exons, I'll focus my response there:
A SNP mapping to an exon might change the amino acid, which might change protein structure and then alter protein function.
A SNP mapping to an exon might not change the amino acid and be called a synonymous SNP. There is evidence that these SNPs can affect translation rates with a concomitant change in protein structure/function (based on codon frequency) and microRNA interactions.
There are also exonic splice enhancers that could be altered by a SNP.
The list will probably grow as we learn more intricacies of gene expression and its regulation.
How about intronic SNPs? Not to expand/change my question post festum, but I'm just now realizing that intronic SNPs are apparently the ones that show the most difference between populations in the paper I'm reading. Why would intronic SNPs be important to track, as they're not changes that are being translated?
You'll find detailed responses elsewhere on this forum. Briefly, an intronic SNP may be exonic in another gene or alt spliced mRNA; affect mRNA splicing vie intronic elements (splice enhanceer, splice site, etc); may affect transcription factor binding (yes TFs bind to introns); among others. Intronic SNPs are important to track as markers and because of the potential to affect gene expression.
A SNP is what the acronym stands for Single Nucleotide Polymorphism, which is in the most straightforward way a polymorphism at a position compared to other sequences and there are no assumptions to what it would normally do.
Now whether its synonymous or nonsynonymous depends on how the codon which has this SNP codes for. And as the name suggests if there's no change in the amino acid its synonymous or else nonsynonymous. There is no particular evidence that nonsynonymous SNP's would be rare...
Note of caution: some people use the "s" differently. At UCSC it means "simple" which can be longer than a single nucleotide. Even dbSNP changed their tag line recently to reflect that.
@douglitas there is a discussion here that you may find useful: http://biostar.stackexchange.com/questions/4835/synonymous-and-non-synonymous-snps