Why does dbsnp Gene View show far less snp ids than the entrez query?

Question

[arronslacey]

Hi - I am having trouble getting my head around something probably very basic. When I go to dbsnp and search for a gene, I get lots of snp ids presented - if I click the "gene view" link, the resulting page provides a list of what it calls all known snps for that gene. The problem I am having is that, the number snps listed in gene view far less than the number of snps presented when simply searching dbsnp using a gene name. why is this?

I have a feeling I'm going to feel very stupid very soon.......

[Pierre Lindenbaum]

an example of gene ? did you restrict your search to only one organism ?

[arronslacey]

yes human only. for example search for GLRA3 in dbsnp

http://www.ncbi.nlm.nih.gov/snp/?term=(human%5BOrganism%5D)+AND+GLRA3%5BGene+Name%5D

which has 4736 snp ids (4058 active) click on gene view (used first occurrence)

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?geneId=8001

and well........there are far less. I am only clicking on gene view because http://www.ncbi.nlm.nih.gov/guide/howto/view-all-snps/ says that is how I get all SNPs associated with a gene

Answer 1

[Pierre Lindenbaum]

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?geneId=8001 only shows the SNPs in the CDNA. selecting "in gene region" returns 4056 snps

[arronslacey]

thanks Pierre - when you perform SNP analysis for a gene (i,e. analyse all variants in a gene), which do you use? it makes sense to me to be using the gene region as these SNPs are known to have been expressed, however papers I am reading generally only describe the cDNA SNPs.