A primary function of the SNPs3D resource is to provide a way of identifying those non-synonymous SNPs that are likely to have a deleterious impact on molecular function in vivo, so these may be included in association studies. An analysis of the likely functional impact of all human non-synonymous single base variants in the HGMD (as of 02/09/2002, 9,625 variants in 696 genes) [1] and dbSNP (Build 124, 29,485 SNPs in 11,303 genes) databases [2,60] is provided, using the previously developed methods [24,25]. Links to another available analysis [26,27] are also included. The analysis is organized by gene. The structure/stability method (23[24]) requires knowledge of structure. Availability of experimental structures or sufficiently accurate structure models limits coverage to about 37% of monogenic disease variants in HGMD and 10% of variants in dbSNP. Greater availability of sequence information compared to structure allows a much higher fraction of variants to be analyzed (92% and 57% HGMD and dbSNP respectively) with the sequence profile method.
