Would you mind walking me trough it in this example??? I don't know how to translate that explanation to real example. So step by step once I am in dbSnp there is a lot of information but I don't see how to determain the mutation. When I read and reaserch the gene only says if the gene is mutated, does not explain for me how to know that or what values to compare to.
http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs1054480
If you click on any of the blue titles it takes you to an information page that explains the display.
At the top of the page in the box under the heading Allele:
Variation class SNV - single nucleotide variation in this instance. Sometimes it can be an insertion or deletion variation instead.
RefSNPAlleles C/T (REV) - this tells you that on the reverse strand C or T are the usual results
Ancestral Allele C - the ancestral allele is the original. It's usually, although not always, the most common and may or may not be the better one to have
Clinical source - if an allele has significance data then there is often a link here to Variation viewer and OMIM with more information on the SNP and/or the gene
Clinical significance N/A - in this instance there is no clinical significance data for this SNP. The kind of information usually found here would be "with pathogenic allele" in red if it has a known detrimental effect
MAF/MinorAlleleCount A 0.252/549 - this is usually reported forward so the A here corresponds to the T above. This tells you that A(T) has a prevalence of 25.2% in the 1000 genome project data, and that A(T) was seen 549 times.
Under the heading Gene View:
If you click on the button "GO" it takes you to a table of SNPS for that gene. There is useful information here too.
Yellow shows snps in the intron region - the effect of these is less known and mostly not significant.
Green shows snps that don't change the gene product - sometimes these make a small difference to the speed of a gene's action but don't change what the gene does.
Red shows snps that are "missense" meaning that the change in allele results in a change to the protein produced. This can result in a gene that does not do what it is supposed to or does not do it efficiently. The table includes if a change is known to be pathogenic.
This table is one of the ways to find rs numbers for snps that 23andme have as i numbers because you can identify them by the position number instead.
Back to the original page, still under gene view:
Under the subheading Gene Model(s)
Function - tells you this is a missense mutation
Allele change - shows you the change from C to T. This is in red because it is a missense mutation.
(Protein) position 1177, (MRna) position 3631 - useful to know for further research with an alternative naming convention
Residue change - the protein coded by the original is Proline (Pro) and the mutation changes it to Serine (Ser)
The table display has coloured boxes which you can click on for more information and links to research if there is any known. I can't use these on my ipad, only on the computer. Purple means known pathogenic. I can't remember what the other colours mean but they are significant.
Under the heading population diversity:
You can see how common the alleles are in populations of various ethnicities. An allele that is common overall may be almost non-existent in some races, or it may be rare overall but common in a particular populations. Some snps have been studied a lot simply because they are useful in determining ancestry rather than of any significance medically. A wide divide in prevalence here can be a clue to that.
If a snp is well studied and known to be associated with something there will most likely be plenty of links on this page to follow up. Sometimes research records the rs number but often not, so it is useful to learn the alternative ways a snp might be displayed if your search doesn't turn up much.
They are often written by the protein change - so in this instance you would find it as Pro1177Ser or P1177S
Sometimes it is reported by the allele change - so by the gene position 3631 you would find it as C3631T or 3631C>T.
Hope that goes some way to answering your question. I found it rather overwhelming when I first started looking but I am learning slowly. A year ago I didn't know any of this.