Nomenclature For Alleles

Question

[jspencenumber29]

How is the nomenclature of an allele derived. For an example the snp in MCPH1 is referred to as G37995C is the G the ancestral allele or is it the derived allele? I need this for my science fair project so please help me! Thanks

Answer 1

[Philipp Bayer]

G37995C means, in this case:

37995 is genomic position on the Microcephalin-gene. G and C are the involved nucleotides: G is the ancestral/major nucleotide, C is the high frequency variant that changes an aspartate to a histidine and may be under positive selection. Hope this helps a bit.

Source

Answer 2

[Mary]

If you want the official guidelines you should check out the HGVS, Human Genome Variation Society: main site = http://www.hgvs.org/rec.html They are the ones who evaluate the issues around this and try to encourage people to use the correct designations. (But a lot of scientists don't even really do this correctly and we drive each other crazy anyway.)

Excruciating details: http://www.hgvs.org/mutnomen/ and click on the various items. A good place to reference in your project.

Good luck at your science fair!

EDIT as an afterthought: you might also want to know that group is distinct from the HGNC or the Human Gene Nomenclature Committee: http://www.genenames.org/ But they work in concert with each other.

Answer 3

[jxchong]

Hmm, actually it depends on where you got that nucleotide change and who was writing it. The G could be any of these things: 1) ancestral allele 2) reference genome allele 3) major allele. These three things are not necessarily the same allele at a given position!