Single-nucleotide polymorphisms (SNPs) are variations at one nucleotide position in the DNA sequence of individuals within a species. They contribute to genomic diversity because individuals of the same species share most of their genome but differ at some nucleotide positions.
How SNPs Arise
A SNP originates through a base substitution mutation, in which one nucleotide is replaced by another. If the altered DNA is inherited and becomes present among individuals in a population, that position can exist in alternative forms.
For example, individuals might have either of these sequences at the same genomic location:
- Individual 1:
AAGCCTA - Individual 2:
AAGTCTA
The sequences differ by one nucleotide: C has been replaced by T. This single difference is a SNP.
Possible Effects of a SNP
The effect depends on where the SNP occurs and whether it changes genetic information used in protein synthesis.
| Location or outcome | Possible consequence |
|---|---|
| Outside a protein-coding sequence | It may have no effect on a polypeptide’s amino acid sequence. |
| Within a codon, but the new codon specifies the same amino acid | No amino acid changes because of the degeneracy of the genetic code. |
| Within a codon that now specifies a different amino acid | The polypeptide’s primary structure may change, potentially affecting protein function and phenotype. |
A common misconception is that every SNP causes disease. Most SNPs are neutral, although some influence phenotype or susceptibility to particular conditions.
This content is assessed at both SL and HL, especially in A3.1 Diversity of organisms and D1.3 Mutation and gene editing. In an exam, define a SNP precisely as variation at one nucleotide position and link it to a base substitution. If asked to explain its effect, trace the sequence: altered DNA base → possibly altered mRNA codon → possibly altered amino acid → possible change in protein structure or function.