Human Gene Mutation Database (HGMD)
- Certain features require login to a personal User Account. These include the ability to save data, access to the Advanced Search function, and the Mutation Viewer. Create your account here. If you need to reset your password, do so here.
- The Mutation Viewer feature requires using the Internet Explorer browser on a Windows PC, Safari on Mac OS systems, or SeaMonkey Browser, formerly the Netscape browser, on either Mac or Windows operating systems.
HGMD offers an extensive set of help guides.
- The Global Documentation manual thoroughly covers HGMD usage, particularly the various search options. It is available either as an HTML document or in PDF format.
- A FAQ resource covers the most common questions.
- Symbols used within HGMD
- Short video tutorials (3-6 minutes) focus to specific search functions and types of records retrieved:
- Chapter 1, “Using Databases” in Current Protocols in Bioinformatics (UB ONLY) covers searching in various bioinformatics databases, including HGMD (Unit 1.13).
HGMD, UB ONLY, manually curates from the peer-reviewed published literature nuclear gene lesions responsible for causing human inherited disease along with any associated polymorphisms. HGMD does NOT include somatic, mitochondrial mutations, pharmacological variants or common, non-disease causing variations. Use COSMIC (Catalog of Somatic Mutations in Cancer) if you are interested in somatic mutations, MitoMap for mitochondrial mutations, PharmGKB for pharmaceutical variants, and NCBI’s dbSNP for single nucleotide polymorphisms.
The mutation data is divided between micro lesions (20 base pairs or less, constituting >85% of all records) and gross deletions (>20 base pairs).
Types of mutations include:
- base pair substitutions, frameshifts and splicing in coding and regulatory gene regions (intronic, extronic, 5’UTR, 3’ UTR)
- micro-deletions, micro-insertions, micro-insertions/deletions
- gross deletions, gross insertions, gross duplications, gross reversions, translocations, complex indels, repeat variations
As of March 2017, there are over 203,855 mutations cataloged in HGMD. Of these, 9,776 have a linked disease-associated phenotype/function record. Approximately half are missense mutations. Most (>88%) have chromosomal coordinates provided.
HGMD has an extensive set of search options.
- Search for mutations in genes, using the HUGO Gene Nomenclature official gene name with the option to specify what type of mutation (missense, indels, etc.).
- Search for mutations at a particular amino acid or chromosomal position via Human Genome Variation Society (HGVS) nomenclature or by chromosomal coordinates.
- Search HGMD’s curated literature by author, publication year, journal name or PubMed ID.
- Find mutations by specifying phenotype.
- Batch searching is available.
- An Advanced Search function permits users to search for mutations by mixing and matching from a multitude of pre-defined or user-specified genomic. These include mutations in either micro RNA or non-coding RNA, mutations in post-translationally modified amino acid residues, mutations at specific amino acid residues or a range of residues, mutations at a specific chromosomal base pair coordinants or a range of base pair coordinates, regulatory sequences (transcription factor binding sites, TATA box, specifying a base pair range upstream and down from a promoter), free text, and more.
- Use of the Advanced Search requires the creation of a user personal account. See the Special Instruction Section above for setting your personal account.
Database established in 1996. It is updated quarterly. An average of 15,000 new mutation entries from the published literature have been added each year for the past six years.
A 2017 review of HGMD thoroughly covers the curation policies, sourcing of mutation data, and classes of variants. PMCID: PMC5429360.