How to use this site

Navigation

Using the gene letter table When you click a letter on the table to the left, you will be shown all genes starting with that letter that have variants associated with them.

Viewing gene variants The “+” sign next to each gene indicates that you can click it to show all variant data. Click the gene again if you want to hide the variants. Your viewing options are remembered the next time you visit that page.

Sorting variant information When viewing variant data for a gene, you can sort the information by clicking the table headers. A arrow indicates descending order. Keep clicking until you see an arrow for ascending order.

Viewing extended annotation data You can view extended annotation data by clicking the small orange box to the left of each row. This opens up the information in a new page. You can either print or download a PDF of the variant of interest.

Seeing quick annotation data To see a ‘quick’ annotation overview, click any part of the row except the orange box. You'll see a popup with the annotation data. To dismiss the popup, click to the top left or anywhere outside the box.

Data

Pathogenicity Assessment

Future versions of the database will be manually curated to incorporate strength of published data about each variant. In silico computational analyses are derived from dbNSFP (link and reference). Pathogenicity is determined as follows:

Polyphen
D – probably damaging > 0.85
P – possibly damaging 0.85 - 0.15
B – benign < 0.15
MutationTaster
Automatically calculated categories: “disease_causing_automatic,” “disease_causing,” “polymorphism,” and “polymorphism_automatic,” which we coded as “A” “D” “N” and “P”. Values closer to 1 have a higher probability that the prediction is true.
PhyloP
C – conserved > 0.95
N – not conserved < 0.95
SIFT
D – deleterious > 0.95
T – tolerated < 0.95
LRT
D – deleterious fulfills the following: (i) from a codon defined by LRT as significantly constrained (LRTorio0.001 and oo1), (ii) from a site with Z10 eutherian mammals alignments, and (iii) the alternative AA is not presented in any of the eutherian mammals.
N – otherwise neutral

Variant Categorization

Pathogenic
mutation published in the literature as causing disease
Probably Pathogenic
classified as such by the dbSNP database
Unknown Significance
variant reported in dbSNP without a disease association

Getting Support

Please get in touch if you experience any issues with using this site.