Intron Variant: Its Impact on Gene Expression and Health

Genetic variations influence gene function, often in ways that are not immediately obvious. While much attention is given to mutations in coding regions, non-coding regions—such as introns—also play a crucial role in gene regulation and expression. Variants in these sequences are increasingly recognized for their impact on health and disease.

Understanding how intron variants affect genetic processes is essential for advancing biology and medical genetics. Researchers continue to uncover how these changes alter gene activity, providing insights into inherited conditions and complex diseases.

Basic Genetics Of Introns

Introns are non-coding sequences within genes that are transcribed into RNA but removed before translation into proteins. Unlike exons, which contain protein-building instructions, introns were once considered “junk DNA.” However, research has shown they serve important regulatory and structural functions. They influence transcription efficiency, alternative splicing, and chromatin organization, all of which contribute to gene regulation.

One key role of introns is in alternative splicing, which allows a single gene to produce multiple protein isoforms. By providing splice sites and regulatory elements, introns enable cells to generate diverse proteins from the same genetic sequence. Variants in these regions can disrupt normal splicing, leading to abnormal proteins that may contribute to disease. Certain intronic mutations have been linked to neurodegenerative disorders and cancer by altering exon inclusion or exclusion in mature mRNA.

Introns also contain enhancer and silencer elements that modulate gene expression. These sequences interact with transcription factors and chromatin-modifying proteins to fine-tune gene activity. Some introns house non-coding RNAs, such as microRNAs and long non-coding RNAs, which influence gene expression by targeting mRNA stability or translation. Additionally, repetitive elements within introns, including transposable elements, can impact genome evolution by introducing new regulatory sequences or affecting chromatin structure.

Role Of Intron Variants In Gene Expression

Intron variants can significantly influence gene expression by altering regulatory elements, splicing mechanisms, and chromatin dynamics. While often overlooked due to their location outside coding sequences, these changes can have far-reaching consequences.

One major way intron variants affect gene expression is by disrupting splicing signals, leading to exon skipping, intron retention, or cryptic splice sites. For example, an intronic variant in the HBB gene associated with β-thalassemia activates an aberrant splice site, generating a nonfunctional hemoglobin protein.

Beyond splicing disruptions, intron variants can interfere with transcriptional regulation by altering enhancer or silencer elements embedded within these regions. Enhancers within introns recruit transcription factors and coactivators, while silencers suppress transcription by binding repressor proteins. Variants that modify these sequences can increase or decrease gene expression. A notable case involves intronic mutations in the FGFR2 gene, which enhance splicing regulator binding and contribute to craniosynostosis syndromes.

Chromatin architecture is also influenced by intron variants, as these sequences contribute to genome folding. Chromatin loops anchored within introns bring distant regulatory elements into proximity with gene promoters, facilitating transcriptional control. Variants in these regions can disrupt chromatin organization, altering gene accessibility. Studies have shown that certain intronic variants in the MYC oncogene influence chromatin conformation, affecting MYC expression and tumorigenesis.

Types Of Intron Variants

Intron variants take multiple forms, each with distinct consequences for gene expression and function. These changes may involve single-nucleotide substitutions, insertions or deletions, or alterations in repetitive sequences. Depending on their location, these variants can influence splicing, transcription efficiency, and chromatin structure, potentially contributing to disease.

Single-Nucleotide Changes

A single-nucleotide variant (SNV) within an intron can have significant effects if it occurs in a functionally important region, such as a splice site or regulatory element. These changes may disrupt normal splicing by weakening or strengthening splice donor and acceptor sites, leading to exon skipping, intron retention, or cryptic splice site activation.

For example, an intronic SNV in the NF1 gene creates a novel splice site, causing the inclusion of intronic sequences in mature mRNA and contributing to neurofibromatosis type 1. Additionally, SNVs can alter transcription factor binding within introns, modifying gene expression. A study in Nature Genetics (2020) identified an intronic SNV in the TERT gene that enhances transcriptional activator binding, increasing TERT expression and cancer risk. These findings highlight the significant impact of single-nucleotide changes in introns.

Insertions Or Deletions

Insertions or deletions (indels) within introns can disrupt gene expression by altering splicing signals or regulatory elements. If an indel occurs near a splice site, it may shift exon-intron boundary recognition, leading to abnormal mRNA processing.

A well-characterized example is an intronic deletion in the SMN2 gene, which affects splicing efficiency and contributes to spinal muscular atrophy. Indels can also modify enhancer or silencer elements, altering transcriptional activity. Large intronic insertions may disrupt chromatin organization, preventing proper gene regulation. Research has shown that an intronic insertion in the F8 gene, responsible for hemophilia A, disrupts normal splicing and reduces functional clotting factor production. These examples illustrate how intronic indels can significantly affect gene function and disease susceptibility.

Repeat Sequence Alterations

Repetitive sequences within introns, such as short tandem repeats (STRs) or transposable elements, can influence gene expression by affecting splicing, transcription, and chromatin structure. Expansions of intronic repeats are particularly well-documented in neurological disorders.

For instance, an expanded GAA repeat in the first intron of the FXN gene leads to transcriptional silencing and causes Friedreich’s ataxia. The expanded repeat interferes with chromatin remodeling, reducing FXN expression and leading to neurodegeneration. Similarly, transposable elements within introns can introduce new splice sites or regulatory sequences, altering gene function. Studies have identified intronic Alu insertions that create cryptic splice sites, leading to aberrant mRNA processing in diseases such as cancer and neurodevelopmental disorders. These findings underscore the role of intronic repeat alterations in shaping gene expression and contributing to disease.

Laboratory Approaches For Identifying Intron Variants

Detecting intron variants requires sequencing technologies, computational analysis, and functional assays. Advances in next-generation sequencing (NGS) have made whole-genome and whole-exome sequencing primary tools for identifying these variants. Whole-genome sequencing captures both coding and non-coding regions, while whole-exome sequencing primarily focuses on exons, often missing deep intronic variants unless specifically targeted. To address this limitation, researchers use targeted sequencing panels designed to cover known intronic regulatory regions and splice sites for more refined analysis.

Once a variant is identified, bioinformatics tools predict its potential effects. Algorithms such as SpliceAI and MaxEntScan assess whether an intronic variant alters splicing by disrupting canonical splice sites or creating cryptic splice signals. Other computational models analyze changes in transcription factor binding within introns. Despite these advances, predictions alone are insufficient for clinical interpretation, necessitating functional validation through molecular assays.

Clinical Relevance In Genetic Diagnosis

Understanding intron variants has become increasingly relevant in genetic diagnosis, as these mutations can influence disease risk, severity, and treatment response. Many inherited disorders once attributed solely to exonic mutations are now recognized to have intronic variants affecting gene function.

In conditions such as cystic fibrosis and Duchenne muscular dystrophy, deep intronic mutations create aberrant splice sites, leading to dysfunctional proteins. Identifying these variants has improved diagnostic accuracy, particularly in cases where traditional genetic testing failed to detect a pathogenic mutation in coding regions. This expanded understanding has also refined genotype-phenotype correlations, helping clinicians predict disease progression based on specific intronic alterations.

Beyond diagnosis, recognizing intron variants has influenced therapeutic strategies, particularly in precision medicine. Splice-modulating therapies, such as antisense oligonucleotides (ASOs), correct aberrant splicing caused by intronic mutations. For example, Spinraza (nusinersen), an FDA-approved ASO for spinal muscular atrophy, targets an intronic regulatory element in the SMN2 gene to enhance functional SMN protein production. Similarly, gene-editing technologies like CRISPR-Cas9 are being explored to correct pathogenic intronic mutations, offering potential curative treatments. As genetic testing becomes more comprehensive, incorporating intron variant analysis into clinical practice will improve diagnostic accuracy and expand therapeutic options for individuals with genetic disorders.