NEWSLETTERS

NEWSLETTER OF THE
HUGO MUTATION DATABASE INITIATIVE
SPONSORED BY THE MARCH OF DIMES (U.S.A)
No.5 July 1998

INSIDE THIS ISSUE:

MUTATION DATABASES AND RELATED RESOURCES
ANNOUNCING NEW MUTATION DATABASES
CORRESPONDENCE
NEW WORKING GROUPS-CALL FOR VOLUNTEERS
CALENDAR OF EVENTS

MUTATION DATABASES AND RELATED RESOURCES

The listing of mutation databases and related resources is now available on the MDI website: http://ariel.ucs.unimelb.edu.au:80/~cotton/dblist.htm Any comments, corrections or additions should be reported to Rania: horaitis@ariel.ucs.unimelb.edu.au

It has been decided that polymorphisms, fashionably known as SNPs should be included in mutation databases.

Artificially induced mutations should also be included in mutation databases as these may be of use to some people. We hope that curators and potential curators include this information in their databases.

ANNOUNCING NEW MUTATION DATABASES

The following databases have recently been released. These are two dbs developed through MDI encouragement and may be linked to from our listing on the web.

Neuronal Ceroid Lipofuscinosis Mutation Database

Genes: CLN1, CLN2, CLN3. CLN4,5,6,7 &8 to come when mutations are found.
http://www.ucl.ac.uk/ncl
Curator: Sara E. Mole, Dept. Paediatrics, Univ College London Medical School, The Rayne Institute, London, UK.
Email: S.Mole@ucl.ac.uk

Retinoblastoma, RB1 Mutation Database.

Gene: RB1
http://home.kamp.net/home/dr.lohmann/
Curator: Dietmar R. Lohmann, Institut fuer Humangenetik, Universitaetsklinikum Essen, Germany.
Email: dr.lohmann@uni-essen.de

CORRESPONDENCE:

REVERSE TRANSLATOR:

http://www2.ebi.ac.uk/cgi-bin/mutations/revtransl.cgi

A simple Web program for calculating the probable DNA point mutations that could have caused the given amino acid substitution. If the reference codon is given, the output includes mutation description in standardised EMBL-like format.

The program is based on a perl function which is available from the author by request.

Heikki Lehvaslaiho
EMBL Outstation, EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge. CB10 1SD, UK.
Fax: 44-(0)-1223-494-468, Email: heikki@ebi.ac.uk

RefGene DATABASE:

The National Center for Biotechnology Information (NCBI) of the National Library of Medicine (NLM) has initiated the RefGene database to catalogue a current and accurate description of proteins and the encoding genes of the human (and mouse) genome. I am coordinating the information on genes and the respective proteins involved with the mitochondria (the mitoDat database, <http://www-lecb.ncifcrf.gov/mitoDat/> was initiated with this in mind, and will be augmented by RefGene, and will serve as an initial resource for RefGene). This list includes proteins localized to the outer membrane, inter-membrane space, inner membrane, and matrix space of the mitochondria. We are exploring a number of avenues to assemble correct information efficiently, and would appreciate the input of the scientific community in this initial endeavor. If you work with a particular protein of the mitochondrion, I would be pleased to receive a paragraph or two from you describing this protein. Please include gene symbol if known, pathway(s) in which the protein is involved, diseases in which the protein is involved if any, and any other information you view as pertinent. Your contribution will be edited and then returned to you for your approval before it is deposited in the RefGene database. If any of your colleagues could help in this endeavor, please make them aware of our desire to assemble an accurate description of proteins important to the mitochondria, certified by the researchers who really know the protein. This database will then have its greatest utility and impact.

Steven J. Zullo
Lab. of Biochemical Genetics, NIMH-NIH; Bldg. 10, Rm. 2D56; 9000 Rockville Pike, Bethesda, MD 20892
FAX: 301-480-9862, Email: zullo@helix.nih.gov

INDEX OF HUMAN PROTEINS WITH SEQUENCE VARIANTS

http://www.expasy.ch/cgi-bin/lists?humpvar.txt

This document is now maintained by Amos Bairoch and currently covers the SWISS-PROT release 35.0 and its updates up to May 1998.

The header of the file describes its contents:
------------------------------------------------------------------------
Total number of human sequence variants currently stored in SWISS-PROT: 6252

For each entry listed, we provide the following information:

1) Primary gene name (generally the official HUGO approved gene symbol);
2) First gene synonym (if any);
3) SWISS-PROT entry name;
4) SWISS-PROT primary accession number;
5) First MIM entry cross-referenced (if any);
6) Number of variants stored in the entry;
7) Disease flag; its presence indicates that at least one of the variant is linked to a disease;
8) 3D flag; its presence indicates that there is at least one 3D-structure entry in PDB for that protein;
9) Xdb flag; its presence indicates that there is at least one cross-reference to a specific Web resource for that protein in that entry.

Heikki Lehvaslaiho
EMBL Outstation, EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge. CB10 1SD, UK.
Fax: 44-(0)-1223-494-468, Email: heikki@ebi.ac.uk

NEW WORKING GROUPS-CALL FOR VOLUNTEERS

We are still looking for volunteers of the new working groups. All are welcome to join the discussion groups:

A. Copyright and Intellectual Property
B. Patient aspects of databases
C. Ethnic and National Databases
D. Polymorphisms/SNP's
E. Quality Control and Peer Review
F. Spectral Databases

CALENDAR OF EVENTS

HUGO MUTATION DATABASE INITIATIVE MEETING

PLACE: Denver, Colorado, U.S.A
TIME: 8.00AM-19.00PM, OCTOBER 27TH 1998
ORGANISERS: R. HORAITIS, R.G.H. COTTON (AUSTRALIA)
TO REGISTER: CONTACT R. HORAITIS
EMAIL: horaitis@ariel.ucs.unimelb.edu.au
FAX: 61-3-9288-2988