If you’ve ever delved in the universe of genetic variants and their potential clinical effects, you most likely have quickly realized that there are lots of databases that store this type of data.
However, and as usual, the contents of these databases are all over the place with respect to how they present their data and the terminology the use. This makes the process of obtaining a single, integrated view of all variants observed in humans a difficult enterprise, even when restricting oneself to public sources.
The good folks at Invitae have gone a fairly long way toward addressing these issues by providing CLINVITAE, a search engine that operates on a large number of variant sources (see list below). There’s no way to know the fraction of the known variant space CLINVITAE covers, but it’s clearly a lot.
The search engine is very friendly (basically modeled on Google’s), making it quite suitable for one-off queries. Furthermore, they also allow downloading of the entire database. As a computational biologist, I can tell you that this is a very nice service indeed, and I salute the company for doing so!
Sources of human genetic variants stored in CLINVITAE:
- Emory Genetics Laboratory Variant Classification Catalog
- ARUP Mutation Databases
- Carver Mutation Database
- Kathleen Cunningham Foundation Consortium for Research into Familial Breast Cancer