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New mutation nomenclature | HGVC July 19, 2007

Posted by ramunas in BRCA, cancer genetics, genetic testing.
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Those working with BRCA1/2 genes probably already know that new mutation nomenclature was proposed by Human Genome Variation Society (HGVC): the nucleotide numbering is from nucleotide 1 of the full gene sequence (Genbank: U14680/ BRCA1; U43746/ BRCA2) not the ATG initiator codon, as is used in biggest repository for BRCA mutations Breast Cancer Information Core (BIC). It creates a lot of confusion, since the old approach prevailed in research articles and clinical application. A new classification includes the true position of nucleotides in deletions or insertions, cause if you have, for example deleted C in a sequence ACC[C]C, the old classification truly do not show which C is deleted (you simply can not discriminate it looking at a sequence – it could be any of these four). Therefore, for example famous Ashkenazi mutations now should be described as follows:

  • BRCA1: 185delA –> c.68_69del (2 exon)
  • BRCA1: 5382insC–> c.5266dup (20 exon)
  • BRCA2: 6147delT –> c.5946del (11 exon)

Now some articles list old nomenclature in parentheses or uses only new or old classification. To define what accession number you’re useing is important, cause there are slight differences – just compare NM_000059 and U43746 of BRCA2. Its still difficult for me to switch to a new variant. I am used to rely on BIC approach. Can you remember, e.g. this masterpiece – c.533-36_5407+400del ? It looks like a free telephone number, doesn’t it? 🙂

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Comments»

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2. drcancer - December 9, 2010

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