Tools

Core A - Variant Curation & Prioritization Core

This application is used by the Variant Curation & Prioritization Core (Core A). This tool will be used to catelog variants in the epilepsy-associated voltage-gated ion channel genes, prioritize variants in ion channel genes for functional evaluation and use functional data to iteratively refine variant classifications and diagnostic criteria. Link↗

Simple ClinVar

Simple ClinVar is a web-based application that is able to provide variant, gene, and disease level summary statistics based on the entire ClinVar database in a dynamic and user-friendly web-interface. The application is able to interactively answer basic questions regarding genetic variation and its known relationships to disease. The website follows ClinVar monthly releases and provide easy access to the rich ClinVar resource to a broader audience including basic and clinical scientists. Link↗

MISCAST

MISCAST is an online resource developed at the Stanley Center in the Broad Institute of MIT and Harvard, by a combined effort from the Genetics and Therapeutics group. The goal of MISCAST is to interpret single amino-acid-altering missense variants on protein 3-dimensional structure and to thereby forecast their biological impact. Link↗

PER viewer

Explore pathogenic variant enriched regions (PERs) across genes and gene families. PER viewer is a tool for missense variant interpretation. Conserved amino acids among gene-family members are enriched with patient variants and constrained from variants in the general population, here we provide a statistical framework that is able to identify PERs across genes and gene families. Link↗

Human Phenotype Ontology Viewer

The Human Phenotype Ontology (HPO) is a formal ontology (vocabulary) of phenotypic abnormalities and clinical features encountered in human disease. It provides a "comprehensive bioinformatic resource for analysis of human diseases and phenotypes and serves as a computational bridge between genome biology and clinical medicine" (Köhler et al., 2017). Link↗

VarTracker

VarTracker is an online tool for searching multiple public genetic variant databases, displaying genetic variant information merged from a variety of sources. The end-user can search for variants of interest based on a RefSeq ID or Gene, and a cDNA change, and the tool will search and extract data from a variety of public databases, such as ClinVar, NCBI Gene, UniProt, dbSNP, NCBI Books, PubMed, MalaCard, MyVariant, gnomAD, ExAC, Mutalyze and ENSEMBL. Link↗