PTCH1 Mutation Database

NAR Molecular Biology Database Collection entry number 147

Database Description

The PTCH1 Mutation Database is a locus-specific database for mutations and SNPs found in the PTCH1 gene. The PTCH1 gene is the human homologue of Drosophila patched, and has been identified as the gene underlying the cancer predisposition syndrome Nevoid Basal Cell Carcinoma Syndrome (NBCCS, OMIM 109400). The PTCH1 gene is believed to function as a tumor suppressor gene and mutations have been found in sporadic basal cell carcinomas, medulloblastomas, as well as other extracutaneous tumors . The database contains just over 200 entries, as of September 2000. Each entry contains information regarding the definition of the aberration, aberration classification, bibliographic data and relevant references. The database user interface is divided into four separate parts; the PTCH1 nucleotide sequence with intron/exon definitions, a primer table with primer definitions for all exons, two query forms - simple query and advanced query, and a submission form where new entries are examined and edited before being made public. The database is based on a generic data model for representing mutation and SNP data implemented by CyberGene. The model is specifically designed with the aim to allow intuitive representation of features characterizing the mutation/SNP. These features include not only obvious ones such as aberration definition, but also characterizations of the aberration''s medical significance. All the features and attributes characterizing a mutation/SNP can be used in queries when information is retrieved from the database. Therefore, it is possible to retrieve information not only based on sequence position or aberration definition, but also based on a mutation characterization composed of the feature values assigned for the mutations/SNPs. A mutation/SNP classification is accomplished by identifying all mutations/SNP sharing common feature values. Hence, a highly dynamic cross-referencing capability is achieved. The database is publicly accessible over the Internet.

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