The GD&P Database
The Genetic Dependence and Pathogenicity (GD&P) Database aims to provide essential information and strategies for evaluating the pathogenic potential of each gene and the pathogenicity/causality of sequence variants from an individual.
The principle of this database is individualizing for each gene and individualizing for each person in evaluating pathogenicity of sequence variants.
The user may start from the home page to search for a gene, getting on to an overview of the gene and then detailed information, which includes general information, genetic dependence data, and evaluation of pathogenic potential of gene and causality of sequence variants.
The general information section provides information on gene function and the related disease, as well as several parameters such as de novo excess, gene damage index, and residual variation intolerance score.
In the genetic dependence section, evidences from inheritance, gene knock-out/knock-in, and functional study are collected to assess the genetic dependence features, including genetic dependence nature (GDN), genetic dependence stage (GDS), and genetic dependence quantity (GDQ). Currently, the GDQs of 109 genes could been quantitatively determined. The GDQ of other genes were grossly classified into high, middle-high, middle, middle-low, or low, based on data of other aspects.
The pathogenic potential of each gene was evaluated from three profiles with a 10-point scoring, including expression, clinic-genetic, and functional studies. In evaluating the pathogenic potential, a scoring of 7/10 or higher could be evaluated as "pathogenic", 5/10-6/10 as "possibly pathogenic", and 3-4/10 as "suspected".
For evaluating the pathogenicity/causality of sequence variants, confirmation of variants' filtering is firstly required. Links to other databases and in silico tools are also available. The user could then evaluate the clinical concordance by comparing the clinic-genetic features of the patient with the pathogenic features of variants of the gene, which have been summarized in four aspects. The causality of the variant is judged according to the criteria presented in the Pathogenicity/Causality of Variants section of the Concept page.