Genome variation can alter not only individual nucleotides but also large chromosome segments. A structural variant changes the arrangement, copy number or chromosomal location of a substantial DNA region.

Four important classes are deletions, duplications, inversions and translocations.

Deletion

A deletion removes a chromosome segment.

A B C D E F → A B E F

Large deletions can remove entire genes or regulatory regions.

Duplication

A duplication creates an additional copy of a segment.

A B C D E F → A B C D C D E F

Duplications change copy number. An extra gene copy can alter the amount of gene product and can also provide redundant sequence that may later accumulate changes independently.

Inversion

An inversion reverses the orientation of a segment within a chromosome.

A B C D E F → A B D C E F

An inversion can disrupt a sequence at its breakpoints or change relationships between genes and regulatory elements even when no DNA is gained or lost overall.

Translocation

A translocation moves a DNA segment to a different chromosomal location. A reciprocal translocation exchanges segments between two chromosomes.

For example,

chromosome 1: A B | C D
chromosome 2: W X | Y Z

             ↓ reciprocal exchange

chromosome 1: A B | Y Z
chromosome 2: W X | C D

How structural variants arise

They can result from incorrectly repaired double-strand breaks, recombination between repeated sequences at non-equivalent positions, replication errors or transposable-element activity.

The molecular mechanism and the final genome structure are different questions. For example, nonhomologous end joining can create a deletion at a repair junction, while misaligned homologous recombination can generate a deletion in one DNA molecule and a duplication in another.

Balanced does not mean consequence-free

An inversion or reciprocal translocation can be balanced, meaning that little or no DNA is lost or gained. Even then, a breakpoint can interrupt a functional sequence or place a gene next to regulatory DNA that normally acts elsewhere.

Structural variation therefore extends the concept of mutation from nucleotide-scale sequence changes to chromosome-scale rearrangements. Later inheritance and cell-division units can reuse these structural definitions without reteaching how the rearrangements themselves are classified.