The human intermediate filament database: Comprehensive information on a gene family involved in many human diseases

Ildiko Szeverenyi, Andrew J. Cassidy, Cheuk Wang Chung, Bernett T. K. Lee, John E. A. Common, Stephen C. Ogg, Huijia Chen, Shu Yin Sim, Walter L. R. Goh, Kee Woei Ng, John A. Simpson, Li Lian Chee, Goi Hui Eng, Bin Li, Declan P. Lunny, Danny Chuon, Aparna Venkatesh, Kian Hoe Khoo, W. H. Irwin McLean, Yun Ping LimE. Birgitte Lane

    Research output: Contribution to journalArticle

    225 Citations (Scopus)

    Abstract

    We describe a revised and expanded database on human intermediate filament proteins, a major component of the eukaryotic cytoskeleton. The family of 70 intermediate filament genes (including those encoding keratins, desmins, and lamins) is now known to be associated with a wide range of diverse diseases, at least 72 distinct human pathologies, including skin blistering, muscular dystrophy, cardiomyopathy, premature aging syndromes, neurodegenerative disorders, and cataract. TO date, the database catalogs 1,274 manually, curated pathogenic sequence variants and 170 allelic variants in intermediate filament genes from over 459 peer,reviewed research articles. Unrelated cases were collected from all of the six sequence homology groups and the sequence variations were described at cDNA and protein levels with links to the related diseases and reference articles. The mutations and polymorphisms are presented in parallel with data on protein structure, gene, and chromosomal location and basic information on associated diseases. Detailed statistics relating to the variants records in the database are displayed by homology group, mutation type, affected domain, associated diseases, and nucleic and amino acid substitutions. Multiple sequence alignment algorithms can be run from queries to determine DNA or protein sequence conservation. Literature sources can be interrogated within the database and external links are provided to public databases. The database is freely and publicly accessible online at www.interfil.org (last accessed 13 September 2007). Users can query the database by various keywords and the search results can be downloaded. It is anticipated that the Human Intermediate Filament Database (HIFD) will provide a useful resource to study human genome variations for basic scientists, clinicians, and students alike.

    Original languageEnglish
    Pages (from-to)351-360
    Number of pages10
    JournalHuman Mutation
    Volume29
    Issue number3
    DOIs
    Publication statusPublished - Mar 2008

    Keywords

    • database
    • intermediate filament
    • keratin
    • desmin
    • lamin
    • GFAP
    • neurofilament
    • epidermolysis bullosa
    • laminopathy
    • C-TERMINAL DOMAIN
    • LAMIN A/C GENE
    • PARTIAL LIPODYSTROPHY
    • DIFFERENTIAL-DIAGNOSIS
    • MONOCLONAL-ANTIBODIES
    • ROD DOMAIN
    • MUTATIONS
    • PROTEINS
    • SEQUENCE
    • LAMINOPATHIES

    Cite this

    Szeverenyi, I., Cassidy, A. J., Chung, C. W., Lee, B. T. K., Common, J. E. A., Ogg, S. C., Chen, H., Sim, S. Y., Goh, W. L. R., Ng, K. W., Simpson, J. A., Chee, L. L., Eng, G. H., Li, B., Lunny, D. P., Chuon, D., Venkatesh, A., Khoo, K. H., McLean, W. H. I., ... Lane, E. B. (2008). The human intermediate filament database: Comprehensive information on a gene family involved in many human diseases. Human Mutation, 29(3), 351-360. https://doi.org/10.1002/humu.20652