Mutations may involve whole chunks of chromosome, rather than single bases.
A length of chromosome may be translocated to another place on the chromosome, or be inverted. Whole chromosomes may fuse, as has happened in primate evolution; chimpanzees and gorillas have 24 pairs of chromosomes whereas humans have 23. In other cases, some or all of the chromosomes may have been duplicated.
It is more difficult to generalize about the phenotypic effects of these chromosomal mutations. If the break-points of the mutation divide a protein, that protein will be lost in the mutant organism. But if the break is between proteins, any effect will depend on whether the expression of a gene depends on its position in the genome.
In theory, it might not matter whether a protein is transcribed from one chromosome or another; though in practice gene expression is probably at least partly regulated by relations between neighboring genes and a chromosomal mutation will then have phenotypic consequences.
A number of chromosomes making up a genome are shown opposite.
An animation shows the different types of chromosome mutations.