A person’s genetic code, or DNA, provides the instructions for building and operating their body. These instructions are contained within genes, which are composed of sections called exons and introns. Exons are the protein-coding sequences, while introns are non-coding segments interspersed between them. An intronic variant is a change in the DNA sequence that occurs within an intron. While once dismissed, it is now understood that introns have functions in regulating gene activity.
The Function of Introns in Genes
A gene can be thought of as a recipe for a protein, with the exons being the cooking instructions and the introns as extra notes in the margins. Before the recipe can be used, these notes must be removed to create a clear, final version. This biological editing process is known as RNA splicing. During gene expression, the entire gene is copied into a precursor molecule called pre-messenger RNA (pre-mRNA).
This pre-mRNA molecule then undergoes splicing. A complex molecular machine called the spliceosome recognizes specific signals at the boundaries of each intron. It cuts the introns out and joins the exons together. This creates a mature messenger RNA (mRNA) molecule.
The resulting mRNA molecule serves as the final blueprint that a cell’s protein-making machinery reads to build a specific protein. This process also allows for alternative splicing, where different combinations of exons can be joined together from the same gene. This enables a single gene to produce multiple different proteins, adding versatility to how genetic information is used.
How Intronic Variants Impact Gene Expression
The precise removal of introns is dependent on specific DNA sequences that mark the beginning and end of each intron. A variant that alters these splice sites can prevent the splicing machinery from recognizing where to cut. This can lead to two primary errors: an entire exon might be skipped, or a whole intron may be incorrectly included. Both outcomes result in an altered mRNA blueprint, which leads to the production of a non-functional or faulty protein.
Another way intronic variants can disrupt gene expression is by creating cryptic splice sites. These are sequences within an intron that closely resemble true splice sites but are normally ignored. A single DNA base change can make a cryptic site more attractive to the spliceosome than the authentic site. This tricks the machinery into cutting at the wrong location, leading to the inclusion of a piece of the intron into the final mRNA. This insertion disrupts the protein’s structure and function.
Introns also contain regulatory sequences that act like volume controls for genes, such as enhancers or silencers. Enhancers increase a gene’s activity, while silencers decrease it. A variant within one of these regulatory elements can disrupt its function. This could cause a gene to be turned on too much, too little, or at the wrong time, contributing to disease even if the protein’s structure remains unchanged.
Identifying and Classifying Intronic Variants
Intronic variants are identified through comprehensive genetic testing methods. While traditional sequencing focused only on exons, newer techniques like whole-genome sequencing (WGS) analyze an individual’s entire DNA sequence, including all introns. This allows for the detection of variants located deep within these non-coding regions. Once a variant is identified, the challenge lies in determining its effect.
Geneticists classify variants into three main categories. A “pathogenic” classification means there is strong evidence the variant is disease-causing. A “benign” classification indicates strong evidence that the variant is harmless. Many intronic variants fall into the category of a “Variant of Uncertain Significance” (VUS).
A VUS designation means there is insufficient information to determine whether the variant is pathogenic or benign. Classifying intronic variants is difficult because their effects on processes like splicing or regulation are harder to predict than those of exonic variants. This uncertainty requires further studies to clarify the variant’s role, making the high number of VUS results a challenge in genetic diagnostics.
Diseases Associated with Intronic Variants
Specific changes within introns have been linked to a range of genetic disorders. These “deep intronic” variants, located far from the exon-intron boundaries, can cause disease by disrupting the gene-to-protein production line. For instance, some cases of cystic fibrosis are caused by an intronic variant in the CFTR gene. This variant creates a new splice site, causing a non-functional protein to be produced.
Similarly, a well-known cause of the inherited anemia beta-thalassemia is a point mutation within an intron of the HBB gene. This change leads to incorrect splicing of the messenger RNA, severely reducing the production of beta-globin protein. Neurofibromatosis type 1 can also result from deep intronic variants that activate cryptic splice sites, leading to a faulty neurofibromin protein.
These examples demonstrate how a single change in what was once considered non-coding DNA can have significant consequences. Variants in genes associated with Duchenne muscular dystrophy, breast cancer, and certain metabolic disorders have also been traced to errors in deep intronic sequences. The study of these variants continues to expand the understanding of genetic disease mechanisms.