Coding variants affect proteins

1. A gene's base sequence determines the amino acid sequence of the protein it codes for.
2. A variant in coding DNA may change the base sequence copied into messenger RNA, written $\mathrm{mRNA}$.
3. When the message is translated at a ribosome, the changed sequence may cause a different amino acid to be added to the protein.
4. The amino acid sequence affects how the chain folds into its specific three-dimensional shape.
5. A change in folding can alter the protein's structure and therefore its activity.
6. The resulting effect on a cell's processes may change the organism's phenotype.

Changes to an enzyme's active site

1. An enzyme binds its substrate at an active site with a complementary shape.
2. If a coding variant changes an amino acid important to folding, the enzyme's active site may change shape.
3. The substrate may then bind less effectively or fail to bind, so fewer enzyme-substrate complexes form.
4. The enzyme-controlled reaction may slow down or stop, changing the amount of product made.
5. If that product is a pigment, a reduced supply can change the colour of a tissue.

Protein changes can alter cells

1. The same reasoning applies to proteins other than enzymes, including transport proteins and structural proteins.
2. A variant affecting haemoglobin can alter how haemoglobin molecules behave and can cause red blood cells to become sickle-shaped under low-oxygen conditions.
3. The example links a DNA difference to a protein difference and then to a change in cell properties.

Non-coding variants affect expression

1. Some non-coding DNA regulates whether a gene is used and how much of its product is made.
2. A variant in a regulatory region can prevent the gene from being transcribed.
3. If transcription is prevented, no $\mathrm{mRNA}$ copy of that gene is produced.
4. Without the $\mathrm{mRNA}$ message, ribosomes cannot make that protein from the affected copy of the gene.
5. Other regulatory changes may increase or decrease transcription, altering the amount of protein produced.
6. A non-coding variant can therefore change phenotype even when the protein-coding sequence itself has not changed.

Distinguishing the two mechanisms

1. A coding variant can change what the protein is like and how effectively it works.
2. A non-coding regulatory variant can change whether, when or how much of a protein is made.
3. Both routes can affect the same characteristic, but the explanation must identify the route supported by the information given.
4. A variant outside an important coding or regulatory sequence may have no detectable phenotypic effect.