Name Generator Exercise

The Mutalyzer Name Generator helps to create sequence variation descriptions in correct HGVS nomenclature syntax. Mutalyzer accepts in principle any Genbank sequence as a reference, but its functionality can be appreciated best using well-annotated genomic reference sequences.

1. Enter the accession number AL449423.14 as a reference sequence.

If you pasted the number into this field, you might see the message "Reference incorrect: should be of the format "NM_002001.2", which will disappear when all spaces have been deleted. Suggestions like these are used to help you specify the correct input.

When the format of the reference sequence is correct, the accession number entered automatically appears a link under the header Constructed HGVS Name. In addition, the form automatically changes to provide variant fields, which have to be filled in before checking the description.

2. Select "genomic DNA" as Sequence Type, select "deletion" as Mutation Type, enter "1" as Start Position, "1" as Stop Position and click on the link under the header Constructed HGVS Name to check with the Name Checker.

The Name Checker output contains a legend describing the transcripts and proteins annotated in the AL449423.14 reference sequence.

3. Copy the annotated transcript and protein information into a separate file (or open a new tab or window).

4. Return to the Name Generator page, now select "coding DNA", enter one of the gene symbols from the legend, and click on the description link to see the effect of a change on the major transcript (optional: enter, in addition to the gene symbol, the number of a transcript variant, e.g., 2 or v002 for the second transcript annotated in the record).

Repeat this for the other gene symbols, additional sequence variation types, changes in introns, across intron exon boundaries, etc. You may check the standard human sequence variant nomenclature guidelines or sequence variation databases for inspiration.