The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies

Abstract

The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.

Fabry Disease: prevalence of affected males and heterozygotes with pathogenic GLA mutations identified by screening renal, cardiac and stroke clinics, 1995–2017

“…Assignment of the phenotype for each GLA pathogenic mutation was based on peer-reviewed publications as listed in the Human Gene Mutation Database (https://portal.biobase-international.com/hgmd/pro/all.php),27 mutation-specific searches of PubMed, review of published clinical information, biochemical findings, in vitro α-GalA expression, structural analyses, and/or relevant clinical and biochemical information from patients seen for over 40 years at the Mount Sinai International Center for Fabry Disease or tested at the Mount Sinai Genetic Testing Laboratory. Each mutation was assigned as Type 1 Classic, Type 2Later-Onset or benign based on available clinical, biochemical and pathological studies (see the International Fabry Disease Genotype/Phenotype Database (dbFGP.org)).…”

Genetic and Phenotypic Characterization of Community Hospital Patients With QT Prolongation

“…Genes and variants that remained after filtering were manually reviewed in the light of available clinical and biological data to evaluate causality. The key tools used for this were Alamut Visual decision‐support software (Interactive Biosoftware), Human Gene Mutation Database,5 and ClinVar 17…”

“…More than 1500 sequence variants in 17 genes have previously been reported to be pathogenic or likely pathogenic for LQTS, although the evidence for some of these is limited 5. Autosomal dominant is the most common inheritance pattern, and KCNQ1 (LQT1) harbors most genetic defects, followed by KCNH2 (LQT2) and SCN5A (LQT3) 6, 7.…”

A Big Data Approach in Mutation Analysis and Prediction

“…[11]. The Human Gene Mutation Database (HGMD) [17] is a database at the Institute of Medical Genetics in Cardiff, from BIOBASE that contains over 152.000 mutations. It is a comprehensive data on human inherited disease mutations to genetics and genomic research.…”