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Exploring a phenotype in chicken

The Rosecomb is a breed of chicken named for its distinctive comb. They are poor egg layers, and not suited for meat production. They are ornamental chickens.

(a) Which gene is associated with the rose comb phenotype?

(b) View sequence variants are associated with this gene. How many are missense? View only these variants.

(c) Are any of these missense variants predicted to cause a deleterious amino acid change?

(a) Go to the Ensembl homepage and search for rose comb.

On the left hand side, click Phenotype to restrict your search results. Click on Rose comb (Chicken Phenotype). Select Rose comb (Chicken Phenotype, Breed: reference).

One gene has been associated with this phenotype. It is ENSGALG00010018369.

(b) Click on ENSGALG00010018369 to go to the Gene tab.

Now click on Variant table in the left-hand menu. Click on the button Consequences: All to filter for consequence types, then select missense variant only.

There are nine missense variants.

(c) SIFT predicts that four variants cause a deleterious amino acid change: rs741576848, rs731357134, rs1058835788 and rs740678215.