The Human Gene Mutation Database: 2008 update
Open accessAbstract
The Human Gene Mutation Database (HGMD®) is a comprehensive core collection of germline mutations in nuclear genes that underlie or are associated with human inherited disease. Here, we summarize the history of the database and its current resources. By December 2008, the database contained over 85,000 different lesions detected in 3,253 different genes, with new entries currently accumulating at a rate exceeding 9,000 per annum. Although originally established for the scientific study of mutational mechanisms in human genes, HGMD has since acquired a much broader utility for researchers, physicians, clinicians and genetic counselors as well as for companies specializing in biopharmaceuticals, bioinformatics and personalized genomics. HGMD was first made publicly available in April 1996, and a collaboration was initiated in 2006 between HGMD and BIOBASE GmbH. This cooperative agreement covers the exclusive worldwide marketing of the most up-to-date (subscription) version of HGMD, HGMD Professional, to academic, clinical and commercial users.
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A fixed-content method appeared impractical for comprehensive carrier screening.
“Given that the Human Gene Mutation Database (HGMD) lists 102,433 disease mutations (27), a number that is steadily increasing, a fixed-content method appeared impractical.”
From Carrier testing for severe childhood recessive diseases by next-generation sequencing (2011) · cites this paper as [27]
The Correspondence section reports that HGMD records disease-associated mutations and that new entries have been increasing, exceeding 9,000 per year. It does not give the cited total of 102,433. The judgment that a fixed-content method was impractical is the citing authors’ inference, not a conclusion attributed to this source. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe Human Gene Mutation Database lists 102,433 disease mutations, and this number is steadily increasing.
“Given that the Human Gene Mutation Database (HGMD) lists 102,433 disease mutations (27), a number that is steadily increasing, a fixed-content method appeared impractical.”
From Carrier testing for severe childhood recessive diseases by next-generation sequencing (2011) · cites this paper as [27]
The Correspondence section says HGMD records disease-causing mutations and that its annual number of new entries has been steadily increasing. Our copy does not report the claimed total of 102,433 disease mutations; the exact figure is therefore unsupported by this citation. (LLM, conf=0.88)
Experimental — accuracy not yet measuredSubstitutions, indels, splicing mutations, and gross deletions account for the vast majority, 96%, of annotated mutations.
“Notably, substitutions, indels, splicing mutations, and gross deletions account for the vast majority (96%) of annotated mutations (27).”
From Carrier testing for severe childhood recessive diseases by next-generation sequencing (2011) · cites this paper as [27]
Two hundred eighty-six severe childhood autosomal recessive diseases encompassed 19,640 known disease mutations.
“Indeed, 286 severe childhood autosomal recessive diseases encompassed 19,640 known disease mutations (8, 27, 28).”
From Carrier testing for severe childhood recessive diseases by next-generation sequencing (2011) · cites this paper as [27]
The Abstract (page unavailable) reports more than 85,000 lesions across 3,253 genes, but does not give a count for severe childhood autosomal recessive diseases. Searches for “286,” “19,640,” and “autosomal recessive childhood disease” found no passage in our copy establishing either claimed figure. (LLM, conf=0.72)
Experimental — accuracy not yet measuredFor array-based screening to be well suited, most carriers must be accounted for by a few mutations, and most disease mutations must be nucleotide substitutions.
“To be well suited for array-based screening, however, most carriers must be accounted for by a few mutations, and most disease mutations must be nucleotide substitutions (8, 27, 28).”
From Carrier testing for severe childhood recessive diseases by next-generation sequencing (2011) · cites this paper as [27]
The Correspondence and Advanced search tools sections describe mutation types in HGMD, but neither discusses when array-based carrier screening is well suited. Searches for array screening and carrier frequency found no passage saying that a few mutations must account for most carriers or that most disease mutations must be nucleotide substitutions. (LLM, conf=0.72)
Experimental — accuracy not yet measured
MutDB holds a much larger set of rare coding variants linked to disease or predicted damaging.
“MutDB112(http://mutdb.org/) contains a much larger number of rare coding variants that are either associated with disease or predicted to be damaging.”
From Rare and common variants: twenty arguments (2012) · cites this paper as [112]
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“Given that the Human Gene Mutation Database (HGMD) lists 102,433 disease mutations (27), a number that is steadily increasing, a fixed-content method appeared impractical.”
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- Authors
- Stenson, P. D., Mort, M., Ball, E. V., Howells, K., Phillips, A. D., Thomas, N. S., & Cooper, D. N.
- Affiliations
- Cardiff University (GB)
- Corresponding author
- Cooper, David N
- Venue
- Genome Medicine
- Published
- 2009-01-22
- Volume
- 1
- Issue
- 1
- Pages
- 13-13
- ISSN
- 1756-994X (ISSN-L)
- DOI
- 10.1186/gm13
- PMC
- PMC2651586
- OpenAlex
- W2158116492
- Cited by
- 873
- References
- 32
- Citations by year
- 2026: 6 · 2025: 8 · 2024: 26 · 2023: 33 · 2022: 18 · 2021: 32 · 2020: 28 · 2019: 35 · 2018: 41 · 2017: 47 · 2016: 73 · 2015: 73 · 2014: 71 · 2013: 102 · 2012: 101
- Type
- conference abstract
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome Medicine (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
- DigitalGeorgetown (Georgetown University Library) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Keywords
- HGMD, germline mutations, genetic disorders, nuclear genes, mutation database, mutational mechanisms, genetic counseling, personalized genomics
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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