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Could someone clearly define what a gene variant is with an example. I am totally confusing myself with SNPs, alleles, variants and how the major and minor allele are defined. A clear example with gene names will be really helpful.

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A fairly easy-to-understand example is that of the ABO blood group system. In this case, there is a single gene involved - ABO, which codes for an enzyme that modifies sugar groups on the surface of red blood cells. This ABO gene has three variants or allelesi, IA, and IB. i (coding for Type O blood) is recessive, which means that its phenotype can only be observed if there are two copies of it – ii – one from the mother and one from the father. IA and IB are co-dominant, meaning that both can be expressed at the same time, and their phenotypes can be observed even if there is only one copy of that allele — for example, IAi would give Type A blood (as would IAIA), IAIB would give Type AB, and so on.

Major and minor alleles (at least in my mind) simply refer to the frequency with which an allele is found in a given population: a minor allele is one that is expressed less-often than a major one. The term minor allele frequency is sometimes used as a numerical representation of expression — a certain allele is only expressed in 3% of the population, for example.

These terms are all from classical genetics — talking about genes and variants without really knowing (or needing to know) what exactly the gene was made up of. Of course, we now know that genes are composed of sequences of DNA nucleotide base pairs (A, T, C, and G), which are then translated by 3bp-codons into proteins, where each codon corresponds to one of 20 amino acids, plus START and STOP sequences. It is in this context of DNA sequence analysis that terms like SNP or Single Nucleotide Polymorphism are used. If you were to compare two alleles, say IA and IB, any single-nucleotide difference between the two could be termed a SNP. Frequently, SNPs are often notated based on the changes the difference would bring to the translated protein sequence — for example, a AAG codon codes for the amino acid lysine, while GAG encodes glutamatic acid. In other cases, a SNP would make no difference to the protein sequence — for example, TTA, TTG, CTC, CTA, CTG, and CTT all encode leucine. You can find the DNA codon table here.

You should keep in mind that SNPs are not the only source of variation in genetic sequences — deletions, translocations, repetitions, inversions, frame shifts, and other mechanisms can all alter the DNA sequence at a particular locus or site. Taken together, all of these differences are often referred to as mutations, which simply means "changes."

I hope this was helpful, please let us know if you still have questions.

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