Many patients suffering from Rare Disease harbour genomic variants (sequence variants or copy number variants) that by disrupting normal gene expression lead to disease. However, many variants are novel or extremely rare, making clinical interpretation problematic and genotype-phenotype correlations uncertain. Identification of patients sharing variants in a given gene and having phenotypic features in common leads to greater certainty in the pathogenic nature of the gene and enables to the role of novel genes in development and disease to be defined. Furthermore, analysis of the type of genomic variant and of its consequence (eg. Loss of function or gain of function) enables insight into the mechanism of disease and potential therapeutic targets.

DECIPHER Project Proposal


DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants.

DECIPHER enhances clinical diagnosis by retrieving information from a variety of bioinformatics resources relevant to the variant found in the patient. The patient’s variant is displayed in the context of both normal variation and pathogenic variation reported at that locus thereby facilitating interpretation.

The DECIPHER Community

Contributing to the DECIPHER database is an international community of academic departments of clinical genetics and rare disease genomics now numbering more than 250 centres and having uploaded more than 27,000 cases. Each contributing centre has a nominated rare disease clinician or clinical geneticist who is responsible for overseeing data entry and membership for their centre. DECIPHER enables a flexible approach to data-sharing. Each centre maintains control of its own patient data (which are password protected within the centre’s own DECIPHER project) until consent is given to share the data with chosen parties in a collaborative group or to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers (see below). Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest.

Public Data Access

With patient consent, positional genomic information together with a brief description of the associated phenotype becomes viewable without password protection, for example, via the DECIPHER track in Ensembl. This is of benefit not only to clinicians advising patients with similar findings but also to researchers working on specific phenotypes, Rare Diseases, drug targets or the role of genes in health and development.