Nonsynonymous Mutation vs. Synonymous Mutation

What's the Difference?

Nonsynonymous mutations and synonymous mutations are two types of genetic mutations that occur in DNA sequences. Nonsynonymous mutations result in a change in the amino acid sequence of a protein, leading to a potentially altered protein structure and function. These mutations can have significant effects on an organism's phenotype and can be either beneficial, detrimental, or neutral. On the other hand, synonymous mutations do not change the amino acid sequence of a protein, as they occur in regions of the DNA that code for redundant codons. These mutations are often considered silent, as they do not affect the protein's function or structure. However, synonymous mutations can still have subtle effects on gene expression, mRNA stability, or protein folding efficiency.


AttributeNonsynonymous MutationSynonymous Mutation
DefinitionA mutation that alters the amino acid sequence of a proteinA mutation that does not alter the amino acid sequence of a protein
Effect on Protein FunctionMay result in a change in protein functionUsually does not affect protein function
Impact on PhenotypeCan have a significant impact on phenotypeUsually has no or minimal impact on phenotype
OccurrenceLess common compared to synonymous mutationsMore common compared to nonsynonymous mutations
Selection PressureSubject to stronger selection pressure due to potential functional consequencesSubject to weaker selection pressure as they are often functionally neutral

Further Detail


Genetic mutations are essential drivers of evolution and can have significant impacts on an organism's phenotype. Two types of mutations that occur within the coding region of genes are nonsynonymous mutations and synonymous mutations. Nonsynonymous mutations result in an amino acid change in the protein sequence, while synonymous mutations do not alter the amino acid sequence. In this article, we will explore the attributes of nonsynonymous and synonymous mutations, their implications, and their roles in genetic diversity.

Nonsynonymous Mutations

Nonsynonymous mutations, also known as missense mutations, occur when a single nucleotide change in the DNA sequence leads to the substitution of one amino acid for another in the resulting protein. These mutations can have various effects on protein structure and function. Some nonsynonymous mutations may be neutral, meaning they do not significantly impact the protein's function or the organism's phenotype. However, others can be deleterious, leading to impaired protein function or even loss of protein activity.

Deleterious nonsynonymous mutations can have severe consequences for an organism's health. They can disrupt critical protein-protein interactions, enzymatic activities, or structural stability, leading to diseases or developmental abnormalities. For example, mutations in the BRCA1 gene, which is involved in DNA repair, can increase the risk of breast and ovarian cancer. These mutations alter the protein's function, impairing its ability to repair damaged DNA effectively.

On the other hand, nonsynonymous mutations can also be beneficial. In certain cases, they can introduce amino acid changes that enhance protein function or confer new functions altogether. These advantageous mutations can provide an evolutionary advantage, allowing organisms to adapt to changing environments. For instance, the sickle cell mutation (Glu6Val) in the hemoglobin gene provides resistance against malaria in individuals heterozygous for the mutation.

Synonymous Mutations

Synonymous mutations, also known as silent mutations, occur when a nucleotide change in the DNA sequence does not alter the resulting amino acid sequence. These mutations typically occur in the third position of a codon, where the genetic code is degenerate. Due to the redundancy of the genetic code, multiple codons can code for the same amino acid.

Unlike nonsynonymous mutations, synonymous mutations are generally considered to be neutral as they do not directly affect protein structure or function. However, recent studies have revealed that synonymous mutations can have subtle effects on gene expression and protein folding. Synonymous mutations can influence mRNA stability, translation efficiency, and even protein folding kinetics. These effects can impact protein levels, localization, and overall function, albeit to a lesser extent compared to nonsynonymous mutations.

Furthermore, synonymous mutations can play a role in the regulation of gene expression. They can affect the binding of regulatory factors, such as microRNAs or RNA-binding proteins, to the mRNA molecule. This modulation of gene expression can have significant consequences for cellular processes and organismal development. Synonymous mutations can also influence the speed and accuracy of translation, affecting the protein's folding and assembly process.

Genetic Diversity and Evolution

Nonsynonymous and synonymous mutations contribute differently to genetic diversity and evolution. Nonsynonymous mutations are more likely to be subject to natural selection due to their potential impact on protein function. Deleterious nonsynonymous mutations are often eliminated from the population through purifying selection, as they reduce an organism's fitness. Conversely, advantageous nonsynonymous mutations can undergo positive selection, spreading through the population and providing an adaptive advantage.

Synonymous mutations, being mostly neutral, are less likely to be subject to strong selective pressures. They can accumulate in the population over time, leading to genetic diversity without significant fitness consequences. Synonymous mutations can serve as molecular markers for studying population genetics and evolutionary relationships between species. By comparing the frequency of synonymous mutations in different populations, scientists can infer the genetic relatedness and divergence times between organisms.

Experimental Detection and Analysis

Distinguishing between nonsynonymous and synonymous mutations is crucial for understanding their functional implications. Several computational algorithms have been developed to predict the impact of nonsynonymous mutations on protein structure and function. These algorithms utilize various features, such as evolutionary conservation, physicochemical properties, and structural information, to assess the potential deleteriousness or beneficialness of a mutation.

Experimental techniques, such as site-directed mutagenesis and functional assays, are also employed to validate the effects of nonsynonymous mutations. These experiments involve introducing specific mutations into the gene of interest and assessing the resulting protein's activity, stability, or interaction capabilities. Additionally, high-throughput sequencing technologies have enabled the identification and analysis of both nonsynonymous and synonymous mutations on a genome-wide scale, providing valuable insights into the genetic variation within populations.


Nonsynonymous and synonymous mutations are two distinct types of genetic alterations that occur within the coding region of genes. Nonsynonymous mutations result in amino acid changes, potentially impacting protein structure and function. They can be deleterious, beneficial, or neutral, depending on the specific mutation and its effects. Synonymous mutations, on the other hand, do not alter the amino acid sequence but can influence gene expression and protein folding to a lesser extent. They are generally considered neutral but can contribute to genetic diversity and serve as molecular markers.

Understanding the attributes of nonsynonymous and synonymous mutations is crucial for unraveling the genetic basis of diseases, studying evolutionary processes, and exploring the functional consequences of genetic variation. By investigating the effects of these mutations, scientists can gain insights into the intricate relationship between genotype and phenotype, ultimately advancing our understanding of life's complexity.

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