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Human Mutation Databases

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The following are a collection of human mutation and SNP databases.

Major databases

[info] The SNP Consortium
[info] dbSNP - A Database of Single Nucleotide Polymorphisms
[info] HGBASE - human genic bi-allelic sequences - SNPs
[info] The Human Gene Mutation Database - HGMD (Cardiff)
[info] Frequency of Inherited Disorders Database (FIDD)
[info] Single Nucleotide Polymorphisms in the Human Genome
[info] Human SNP Database
[info] ALFRED - Allele Frequency Database
[info] Mutation Database Website
[info] Universal Mutation Database
[info] Protein Mutation Database

Specific gene locus databases

[info] The Androgen Receptor Mutations Database
[info] Antithrombin Mutation Database Homepage
[info] Asthma Gene Database
[info] Breast Cancer Mutation Data Base (BIC)
[info] BCGD - The Breast Cancer Gene Database
[info] BIOMDB - Database of mutations causing tetrahydrobiopterin deficiencies
[info] Blood Group Antigen Mutation Database
[info] BTKbase - agammaglobulinemia XLA-causing mutations
[info] The European CD40L Defect Database (CD40Lbase)
[info] Database of Human Type I and Type III Collagen Mutations
[info] Emery-Dreifuss Muscular Dystrophy Mutation Database
[info] Factor VII Mutation Database
[info] GPCRmut, The G Protein-Coupled Receptors mutant database
[info] GPCRDB: Information system for G protein-coupled receptors (GPCRs)
[info] GRAP Mutant Database (GPCRs, Family A)
[info] Haemophilia B Mutation Database
[info] HAMSTeRS - Haemophilia A Mutation, Search, Test and Resource Site
[info] Human HPRT database
[info] Hypertrophic Cardiomyopathy mutation database
[info] LDLR Mutation Database
[info] Long QT syndrome database
[info] Marfan Database
[info] MutRes - List of Mutation Resources
[info] Neuronal Ceroid Lipofuscinoses (NCL) Mutations
[info] PAH Genes and alleles (PAHDB)
[info] Human p53 database
[info] p53 gene mutations
[info] Somatic p53 mutations in human tumors and cell lines.
[info] Database of germline p53 mutations
[info] p53link - P53 database integration
[info] PAX2
[info] PAX6 mutation database
[info] Schindler Disease
[info] VHL Mutation Database
[info] VMD2 Mutation Database
[info] von Willebrand Factor (vWF) Database
[info] WS-associated WRN mutations

Detailed information on the above options

The SNP Consortium
A non-profit foundation set up by the Wellcome Trust and various pharmaceutical companies to develop up to 300,000 SNPs distributed evenly throughout the human genome and to make the information related to those SNPs publicly available. The data are also submitted to dbSNP.

dbSNP - A Database of Single Nucleotide Polymorphisms
In collaboration with the National Human Genome Research Institute, The National Center for Biotechnology Information has established the dbSNP database to serve as a central repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. Once discovered, these polymorphisms could be used by additional laboratories, using the sequence information around the polymorphism and the specific experimental conditions. (Note that dbSNP takes the looser 'variation' definition for SNPs, so there is no requirement or assumption about minimum allele frequency.) The data in dbSNP will be integrated with other NCBI genomic data. As with all NCBI projects, the data in dbSNP will be freely available to the scientific community and made available in a variety of forms.

HGBASE - human genic bi-allelic sequences - SNPs
HGBASE lists human intra-genic promoter to transcription end point DNA sequence polymorphisms. It has been constructed by The Department of Genetics and Pathology at Uppsala University and Interactiva Biotechnologie GmbH. HGBASE does not include gene mutations, but is a catalogue of intra-genic sequence variants found in normal individuals. Despite its name, HGBASE contains all types of gene based variation and is not limited to bi-allelic Single Nucleotide Polymorphisms SNP s. Functionally consequential polymorphisms e.g. promoter and non-silent codon changes and other polymorphisms e.g. intron sequence differences are included.

Search tools are provided to find data within HGBASE. Searches utilise a text string or a DNA sequence. Data submission is by a series of Web page data submission forms. All submitted data is made available to other public databases. The exponential growth in polymorphism discovery requires that scientists make every effort to submit their data to HGBASE to ensure it remains up to date. HGBASE does not claim any rights to publicly available or submitted data, instead this remains the property of the original submitter/discoverer. Deposition of data within HGBASE requires only the allelic DNA sequence, the allele frequencies, the host gene name, and the intra-genic domain. Additional information, such as assay conditions, can be supplied but this is optional.

The Human Gene Mutation Database - HGMD (Cardiff)
This database represents an attempt to collate the majority of known (published) gene lesions responsible for human inherited disease. Originally established for the study of mutational mechanisms in human genes (Cooper and Krawczak 1993), these databases have acquired a much broader utility in that they currently represent the only available comprehensive reference source to the spectrum of mutations underlying human genetic disease. They thus provide information of practical diagnostic importance to (i) researchers in human molecular genetics, (ii) physicians interested in a particular inherited condition in a given patient or family and (iii) genetic counsellors.

Frequency of Inherited Disorders Database (FIDD)
The Frequency of Inherited Disorders Database (FIDD) has been established for use in a clinical context, in medical research, for epidemiological studies, and in the planning of genetic services.

It represents the first easily accessible repository of published data on the frequency of human inherited disorders worldwide. Data collated include the disease categorized by organ system, Online Mendelian Inheritance in Man (OMIM) number, mode of inheritance, population origin, prevalence and/or incidence rate, and a literature reference.

Single Nucleotide Polymorphisms in the Human Genome
This website is designed to provide the human genetics community with access to single nucleotide polymorphism (SNPs) that have been developed as genetic markers on the human genome. The site is organized by chromosomes and cytogenetic location. Each SNP has PCR primer and conditions associated with it.

Currently, we only post the SNPs that we have helped to develop. After we have posted all of our SNPs, we'll be adding SNPs from the literature and from collaborators, and we will be happy to have others contribute to the database.

Human SNP Database
This is the Whitehead/MIT SNP data.

ALFRED - Allele Frequency Database
This gives gene frequency data for a diverse set of population samples and genetics systems.

It contains data on more than 40 populations representing most major regions of the world and data on more than 150 genetic systems including SNPs, STRPs and insertion-deletion polymorphisms.

Mutation Database Website
Information on nomenclature and design of mutation databases.

Universal Mutation Database
Software and databases for mutations in human genes.

Protein Mutation Database
PMD is based on literature (not on proteins); that is, each entry of the database corresponds to one article which describes protein mutations.

The Androgen Receptor Mutations Database
Constitutional mutations in the androgen receptor gene (AR ) impair androgen - dependent male sexual differentiation to various degrees . Somatic mutations in the AR have been found in metastatic prostate cancer. Severe constitutional androgen insensitivity (AI) yields an external female phenotype. Partial constitutional AI yields a range of external genital phenotypes that vary from near - normal female to normal or near - normal male, with or without gynecomastia and other relatively"mild" signs of undervirilization.

Antithrombin Mutation Database Homepage
Antithrombin is a plasma inhibitor of thrombin and other blood coagulation proteinases. Its (functional) deficiency is a strong risk factor for venous thrombosis. The gene coding for antithrombin has been localised to chromosome 1q23-25.

Asthma Gene Database
This is a database for asthma and allergy linkages and mutations.

As you can enter and change data from every part of the world they have implemented password restriction. Registration to this database is free.

Breast Cancer Mutation Data Base (BIC)
A resource for the molecular biologist investigating inherited breast cancer providing a central repository for information regarding breast cancer susceptibility genes mutations and polymorphisms.

This requires you to register as a BIC member.

BCGD - The Breast Cancer Gene Database
Contains information about genes involved in human breast cancer.

BIOMDB - Database of mutations causing tetrahydrobiopterin deficiencies
BIODEF is a locus-specific database with detailed records of disease-producing allelic variations and natural polymorphic markers.

Blood Group Antigen Mutation Database
This database will deal with mutations in loci of allelic genes that specify the common blood group antigens and the allelic variants of those common genes.

BTKbase - agammaglobulinemia XLA-causing mutations
X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK).

A database (BTKbase) of BTK mutations has been compiled and the recent update lists 463 mutation entries from 406 unrelated families showing 303 unique molecular events. In addition to mutations, the database also lists variants or polymorphisms.

The European CD40L Defect Database (CD40Lbase)
X-linked Hyper-IgM syndrome-associated mutation database.

Database of Human Type I and Type III Collagen Mutations
Includes accounts of every known mutation in the genes encoding the alpha-1 and alpha-2 chains of type I collagen

Emery-Dreifuss Muscular Dystrophy Mutation Database
Brief description of mutations.

Factor VII Mutation Database
The Factor VII Mutation Database is currently under construction.

GPCRmut, The G Protein-Coupled Receptors mutant database
Mutation analysis of GPCRs

GPCRDB: Information system for G protein-coupled receptors (GPCRs)
Contains information about GPCR sequences, multiple sequence alignments of GPCR families, 3D models, articles, GPCR mutation data and more.

GRAP Mutant Database (GPCRs, Family A)
A database of mutants of family A G-Protein Coupled Receptors. GRAP contains detailed description of the ligand binding and signal transductional properties.

Haemophilia B Mutation Database
A database of point mutations and short additions and deletions in the factor IX gene.

HAMSTeRS - Haemophilia A Mutation, Search, Test and Resource Site
Over the last decade there has been a dramatic increase in our understanding of the pathology of haemophilia A in molecular terms, at the levels both of nucleic acid sequence and to a much lesser extent, protein structure.

Human HPRT database
The database contains information on the mutagen, dose, spontaneous and induced mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, cell type, citation, and other items. In addition, information regarding the cause and effect of mutations affecting splicing is given.

Hypertrophic Cardiomyopathy mutation database
Familial hypertrophic cardiomyopathy is a genetic disorder associated with defects in the sarcomere.

LDLR Mutation Database
Mutations in the LDL receptor gene (LDLR) cause familial hypercholesterolemia (FH), a common autosomal dominant disorder. The LDLR database is a computerized tool that has been developed to provide tools to analyse the numerous mutations that have been identified in the LDLR gene.

Long QT syndrome database
Long QT syndrome (LQTS) is a heart disease manifesting itself by a prolonged QT interval on the ECG and clinically by a propensity for tachyarrhythmias, causing syncopes and sudden cardiac death.

Marfan Database
The Marfan database is a software that contains routines for the analysis of mutations identified in the FBN1 gene that encodes fibrillin-1. Mutations in this gene are associated not only with Marfan syndrome but also with a spectrum of overlapping disorders.

MutRes - List of Mutation Resources
MutRes is a public list of databases, websites, programs and people related to collection and computational analysis of mutations.

MutRes relies on mutation database community for its accuracy of data. If you know unlisted resources or want to add to an existing entry, please use the MutRes Web submission form.

MutRes is made available through Thure Etzold's Sequence Retrieval System (SRS). It allows full text searching and instant hypertext linking to Web resources.

Neuronal Ceroid Lipofuscinoses (NCL) Mutations
Published mutations and polymorphisms in the NCL genes together with unpublished data included with permission.

PAH Genes and alleles (PAHDB)
Mutation data were collated from both published articles and personal communications of 80 investigators from the PAH Mutation Analysis Consortium in 26 countries.

Searchable fields of the database available to users are: mutation name, polymorphic haplotype, population, geographic location, gene region, codon number, mutation type, substitution, phenotype, and author's name.

Human p53 database
The database contains information on the cancer type, loss of heterozygosity, base position, amino acid position, amino acid change, local DNA sequence,citation, and other items.

p53 gene mutations

Somatic p53 mutations in human tumors and cell lines.
The p53 mutation database contains information on all missense mutations and small deletions reported in human p53 reported in peer-reviewed literature. It does not contain information on p53 mutations in animals nor data on human tumors with no p53 mutations.

Database of germline p53 mutations
A comprehensive database covering all published cases of germline p53 mutations. The current version lists 580 tumours in 448 individuals belonging to 122 independent pedigrees. The database describes each p53 mutation (type of the mutation, exon and codon affected by the mutation, nucleotide and amino acid change), each family (family history of cancer, diagnosis of Li-Fraumeni syndrome), each affected individual (sex, generation, p53 status, from which parent the mutation was inherited) and each tumour (type, age of onset, p53 status-loss of heterozygosity, immunostaining). Each entry contains the original reference(s).

p53link - P53 database integration
Several p52 mutation databases are available in the net. There is no cross-linking between them and consequently it is impossible to know what is the non-redundant set of known mutations in p53.

The goal of p53link is to create links between various p53 databases.

The Human PAX2 Allelic Variant Database.

PAX6 mutation database
Contains data on human PAX6 mutations.

Schindler Disease
Mutations in the a-N-Acetylgalactosaminidase Gene Causing Schindler Disease

VHL Mutation Database
VHL is a tumor suppressor gene localized on chromosome 3p25-26. Mutations of the VHL gene were described at first in the heritable von Hippel-Lindau disease and in the sporadic Renal Cell Carcinoma (RCC). More recently, VHL has also been shown to harbor mutations in mesothelioma and small cell lung carcinoma.

VMD2 Mutation Database
Sequence, mutation and polymorphism data on the VMD2 gene.

von Willebrand Factor (vWF) Database
Databases of point mutations, insertions, deletions, and polymorphisms found in von Willebrand Factor.

WS-associated WRN mutations
Werner syndrome (WS) is one of a group of human genetic diseases that have recently been linked to deficits in cellular helicase function. We review here the structure and expression of the WRN locus, and the spectrum of WS-associated WRN mutations. The organization and potential functions of the WRN protein are discussed, as are potential mechanistic links between mutational inactivation or loss of WRN and pathogenesis of the WS clinical and cellular phenotypes.

Any Comments, Questions? Support@hgmp.mrc.ac.uk