Leiden Muscular Dystrophy pages^©

Gene variant database IDentifiers

(last modified October, 2009)

Introduction

Throughout the gene variant databases covered by the "Leiden Muscular Dystrophy pages (LMDp)", we have assigned a unique LMDp IDentifier (ID) to all gene variants listed. This unique ID will be stable and never change.

Authors submitting sequence variations to the LMDp-databases will receive a confirming message (E-mail), listing the new ID's given. In this way, irrespective of publication in a printed scientific journal, authors will have the possibility to refer to the allelic variants submitted as an electronic publication. References to the mutations can be made in a format like "Den Dunnen JT (2002). 12 new mutations in the DMD-gene. DMD_00083-DMD_0094. Leiden Muscular Dystrophy pages at http://www.DMD.nl/".

Linking direclty to these variants can be through a link with the format;
        url/variants.php?select_db=CAPN3&action=search_unique&search_Variant%2FDBID=CAPN3_00332
linking to the variant CAPN3_00332.

Linking directly to all variants submitted by a specific submitter, e.g. the submitter with ID = 00232, can be through a link with the format;;
       url/submitters_variants.php?genes[]=TPM3&submitterid=00232
linking to variants in the TPM3 gene of submitter 00232.

Format ID

The database ID's have the format "GeneSymbol_code", e.g. SGCD_00005 or DMD_e5e9b.

Change at DNA level fully characterised -  format like GeneSymbol_number, e.g. SGCD_00005

• GeneSymbol
  The GeneSymbol is the official abbreviation for the gene containing the sequence variant, as approved by the Human Gene Nomenclature Committee (HUGO).
• Number
  a unique 5 digit number discriminating all sequence variations in one specific database (assigned by the database curator)

Change at DNA level not fully characterised
Special IDs are used for variants which have not been fully characterized at DNA level, e.g. deletions / duplications identified by Southern blotting or varaints studied at RNA level only.

• format GeneSymbol_00000, e.g. DMD_00000
  DB-IDs with the number "00000" are used for all variants where data at the DNA level is incomplete. They are treated in a special way
  
• format GeneSymbol_code, e.g. DMD_e5e9b
  used to describe deletions/duplications of entire exons without data available on the sequences at the breakpoint.

1. geneID, like "DMD_"
2. first exon affected, like "e5"
3. last exon affected, like "e9" (added only when different from the first exon affected)
4. only for duplications a "b"   (to dicriminate duplications from deletions)

| Top of page | LMDp databases |
| LMDp home page |