Human Mutation Databases

Ourania Horaitis1, Richard G.H. Cotton2

1 Genomic Disorders Research Centre, St. Vincent's Hospital Melbourne Fitzroy, 2 The University of Melbourne, Melbourne
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.10
DOI:  10.1002/0471250953.bi0110s9
Online Posting Date:  April, 2005
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The first part of this unit compares general and locus‐specific mutation databases. The second section deals with submitting data. The third part provides guidance for accessing mutation data. The final section offers advice on database construction.

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Table of Contents

  • Overview
  • Submission of Data to Mutation Databases
  • Accessing Data in Mutation Databases
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

   Antonarakis, S.E. and the Nomenclature Working Group. 1998. Recommendations for a nomenclature system for human gene mutations. Hum. Mutat. 11:1‐3.
   Beroud, C., Collod‐Beroud, G., Boileau, C., Soussi, T., and Junien, C. 2000. UMD (Universal Mutation Database): A generic software to build and analyze locus‐specific databases. Hum. Mutat. 15:86‐94.
   Brown, A. and McKie, M. 2000. MuStaR and other software for locus‐specific mutation databases. Hum. Mutat. 15:76‐85.
   Claustres, M., Horaitis, O., Vanevski, M., and Cotton, R.G.H. 2002. Time for a unified system of mutation description and reporting: A review of locus specific mutation databases. Genome Res. 12:680‐688.
   Cotton, R.G.H. and Horaitis, O. 2000. Quality control in the discovery, reporting, and recording of genomic variation. Hum. Mutat. 15:16‐21.
   Cotton, R.G. and Scriver, C.R. 1998. Proof of “disease causing” mutation. Hum. Mutat. 12:1‐3.
   den Dunnen, J.T. and Antonarakis, S.E. 2000. Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion. Hum. Mutat. 15:7‐12.
   den Dunnen, J.T. and Antonarakis, S.E. 2003. Mutation nomenclature. In Current Protocols in Human Genetics (N.C. Dracopoli, J.L. Haines, B.R. Korf, C.C. Morton, C.E. Seidman, J.G. Seidman, and D.R. Smith, eds.) pp. 7.13.1‐7.13.8. John Wiley & Sons, Hoboken, N.J.
   Fredman, D., Siegfried, M., Yuan, Y.P., Bork, P., Lehväslaiho, H., and Brookes, A.J. 2002. HGVbase: A human sequence variation database emphasizing data quality and a broad spectrum of data sources. Nucleic Acids Res. 30:387‐391.
   Hamosh, A., Scott, A.F., Amberger, J., Valle, D., and McKusick, V.A. 2000. Online Mendelian Inheritance In Man (OMIM). Hum. Mutat. 15:57‐61.
   Horaitis, O., Scriver, C.R., and Cotton, R.G.H. 2001. Locus‐Specific Mutation Databases. In The Metabolic and Molecular Bases of Inherited Disease, 8th ed. (C.R. Scriver, A.L. Beaudet, W.S. Sly, and D. Valle, eds.) Ch. 1, App. 1‐2. McGraw‐Hill, New York.
   Krawczak, M., Ball, E.V., Fenton, I., Stenson, P.D., Abeysinghe, S., Thomas, N., and Cooper, D.N. 2000. Human Gene Mutation Database: A biomedical information and research resource. Hum. Mutat. 15:45‐51.
   Patrinos, G.P., van Baal, S., Petersen, M.B. and Papadakis, M.N. 2005. Hellenic National Mutation Database: A prototype database for mutations leading to inherited disorders in the Hellenic population. Hum. Mutat. 25:327‐333.
   Riikonen, P. and Vihinen, M. 1999. MUTbase: Maintenance and analysis of distributed mutation databases. Bioinformatics 10:852‐859.
   Scriver, C.R., Nowacki, P.M., and Lehväslaiho, H. 1999. Guidelines and recommendations for content, structure, and deployment of mutation databases. Hum. Mutat. 13:344‐350.
   Scriver, C.R., Nowacki, P.M., and Lehväslaiho, H. 2000. Guidelines and recommendations for content, structure, and deployment of mutation databases. II. Journey in progress. Hum. Mutat. 15:13‐15.
   Scriver, C.R., Hurtubise, M., Konecki, D., Phommarinh, M., Prevost, L., Erlandsen, H., Stevens, R., Waters, P.J., Ryan, S., McDonald, D., and Sarkissian, C. 2003. PAHdb2002: What a locus‐specific knowledgebase can do. Hum. Mutat. In press.
   Sipila, K. and Aula, P. 2002. Database for the mutations of the Finnish disease heritage. Hum. Mutat. 19:16‐22.
   Teebi, A.S., Teebi, S.A., Porter, C.J., and Cuticchia, A.J. 2002. Arab genetic disease database (AGDDB): A population‐specific clinical and mutation database. Hum. Mutat. 19:615‐621.
Internet Resources
  AGDDB: Arab Genetic Disease Database
  Blood Group Antigen Mutation Database
  dbSNP: NCBI Single Nucleotide Polymorphism database
  OMIM: Online Mendelian Inheritance in Man
  A Syllabus of Human Hemoglobin Variants and A Syllabus of Thalassemia Mutations
  HGMD: Human Gene Mutation Database
  HGVS: Human Genome Variation Society
  HGVbase: Human Genome Variation Database
  MuStar: Mutation Storage and Retrieval
  MUTbase: Mutation Database
  PAHdb: Phenylalanine Hydroxylase Locus Know ledgebase
  SHOX Mutation Database
  UMD: Universal Mutation Database
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