Aneuploidy usually alters the phenotype drastically. In most animals and many plants, aneuploid mutations are lethal. Because aneuploidy affects the number of gene copies, but not their nucleotide sequences, the effects of aneuploidy are most likely due to abnormal gene dosage. Aneuploidy alters the dosage for some, but not all, genes, disrupting the relative concentrations of gene products and often interfering with normal development.

A major exception to the relation between gene number and gene dosage pertains to genes on the mammalian X chromosome. In mammals, X-chromosome inactivation ensures that males (who have a single X chromosome) and females (who have two X chromosomes) receive the same functional dosage for X-linked genes (see Chapter 4 for further discussion of X-chromosome inactivation). Additional X chromosomes in mammals are inactivated, so we might expect that aneuploidy of the sex chromosomes would be less detrimental in these animals. Indeed, this is the case for mice and humans, for whom aneuploidy of the sex chromosomes is the most common form of aneuploidy seen in living individuals. Y-chromosome aneuploidy is probably common because there is so little information in the Y chromosome.

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