A base substitution changes one nucleotide to another. In a protein-coding sequence, the biological consequence depends on how that change alters an mRNA codon.

Substitutions are also classified by base chemistry:

• a transition replaces a purine with another purine (A↔G) or a pyrimidine with another pyrimidine (C↔T);
• a transversion exchanges a purine for a pyrimidine or vice versa.

This classification describes the DNA change, not its functional effect.

Synonymous substitution

Because the genetic code is degenerate, a changed codon can still specify the same amino acid.

GAA → GAG
Glu → Glu

This is synonymous with respect to the encoded amino acid. Synonymous does not mean that every possible biological effect is absent; it means only that the amino-acid identity is unchanged.

Missense substitution

A changed codon can specify a different amino acid:

GAA → GUA
Glu → Val

This is a missense substitution. Its effect depends on the chemical difference between the amino acids and the role of that residue in the protein.

Nonsense substitution

A substitution can convert an amino-acid codon into a stop codon:

UAU → UAA
Tyr → Stop

This is a nonsense substitution and can terminate translation prematurely.

Thus the same DNA-level event—a single substitution—can be synonymous, missense or nonsense depending on coding context. Sequence-change class and functional consequence are separate levels of description.