RS SNP's to Protein Change name please

Question

[sarah]

Trying to match some RS numbers SNP's to their corresponding protein change name (eg RS 9290264 has a corresponding protein change name v15F), and also some protein change names which i need to find the corresponding RS numbers for. Is there an easy way to do this please? Have searched the NcBI database. Do some RS numbers just not have a protein change name? I am not a scientist or expert, just trying to find a few answers to help my 2 little girls who have a rare genetic condition. Any help would be greatly appreciated, thanks Sarah

[sarah]

thank you, that is very helpful ben thank you for your insight :-)

Answer 1

[benformatics]

Not all RS numbers have a protein change. Since proteins are made up of triplets (e.g. ACG, AGG, etc..) of nucleotides (A,G,C, or T; simplifying a bit), it is possible to have a synonymous mutation. A mutation where the underlying change does not modify the protein produced. The modification could affect any of a variety of molecular biological mechanisms - some of which may not even be completely understood to this day. It really depends on the specific modification. You can actually search for RS numbers on the UCSC genome browser [but you need to remove the space when you type it in (e.g. rs9290264 and make sure you choose the human genome; either hg19 or h38). This should zoom you in to the exact location of the mutation in the genome and let you know what potential gene/protein is effected.

Also, modifications with RS ID's can be directly investigated in dbSNP - one's without, you will need to figure out which gene and/or which genomic coordinates they are found at.

Answer 2

[swbarnes2]

Since many genes have multiple transcripts, there can't be one universal amino acid coordinate for many SNPs. Your case is lucky, there are only 2 protein coding transcripts there, and the numbering of their amino acids is the same at that point

http://uswest.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;r=3:165075470-165076470;v=rs9290264;vdb=variation;vf=40357853

But you can't always expect that.