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Exploring a variant in pig

The human gene MC4R has been associated with obesity. The SNP rs81219178 has been identified as a variant in the pig MC4R gene.

(a) What is the amino acid change caused by rs81219178 in MC4R of the pig? Is the change likely to alter the protein function?

(b) Have genotype frequencies been determined for any pig strains? Which strains? Which genotype is the most frequent?

(a) Go to the Ensembl homepage.

Type rs81219178 in the Search box, then click Go.

Click on rs81219178 (Pig Variant).

Click on Genes and regulation in the left-hand menu or on the icon.

The variant causes a D->N amino acid change (Aspartic acid -> Asparagine). The SIFT score of 0.01 predicts that this change will have a deleterious effect on the protein.

(b) Click on Population genetics in the left-hand menu. (Alternatively, click on Explore this variant at the left and then click on the Population genetics icon.)

Hover over the population names to find out more about the populations.

Genotype frequency is recorded for three pig populations, two Berkshire x Yorkshire populations and one Large White × Landrace population. In all three, the A/G genotype is the most common genotype.