Imagine your genes as a recipe book, and your cells as chefs who can make different dishes from the same recipe by skipping or adding steps. This flexibility comes from a process called alternative splicing, which allows a single gene to produce multiple protein variants—known as splice variants. While this diversity is essential for life, errors in splicing can lead to diseases like cancer, neurological disorders, and immune conditions. Let’s break down what splice variants are, how they alter protein function, and what details scientists analyze to determine if a splice variant poses a health risk.
What Are Splice Variants?
Genes are made of segments called exons (coding regions) and introns (non-coding regions). During gene expression, cells “edit” the raw gene transcript by removing introns and stitching exons together. Alternative splicing allows cells to mix and match exons in different combinations, creating distinct mRNA molecules (and thus proteins) from the same gene (6).
For example, the gene OPN (osteopontin) can produce splice variants like OPN-a and OPN-c. While OPN-a is involved in normal bone remodeling, OPN-c is linked to cancer progression (9, 12).
How Splice Variants Affect Protein Function
Splice variants can drastically change a protein’s structure and role. Here’s how:
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Truncated Proteins: Skipping an exon might delete a critical protein region. In CHEK2 (a cancer-risk gene), a splice variant removes part of the protein, impairing its ability to repair DNA (13).
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Altered Binding Sites: The FGD1 gene’s splice variant in kidney cancer disrupts a protein domain necessary for cell signaling, promoting metastasis to the brain and bones (11).
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Nonfunctional Proteins: Some splice variants include “poison exons” that introduce early stop signals. For instance, a SCN5A splice variant in heart disease produces a shortened protein that disrupts heart rhythms (10).
Even subtle changes matter. The immune receptor IFN-λR1 has a splice variant that produces a shortened, soluble protein. This variant dampens the body’s antiviral response, increasing susceptibility to infections (3).
Deciding If a Splice Variant Is Risky: Key Factors
Not all splice variants are harmful. Scientists evaluate these details to assess risk:
1. Location of the Splicing Error
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Critical Regions: Variants in conserved splice sites (e.g., the “GT” and “AG” boundaries of introns) are more likely to cause harmful skipping of entire exons (4). For example, a PLP1 splice variant disrupts myelin formation in the brain, leading to neurological disorders (2).
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Deep Intronic Changes: Mutations deep within introns can activate “cryptic” splice sites, creating abnormal exons. These are harder to detect but can still produce faulty proteins (4, 6).
2. Type of Protein Change
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Loss of Function: If the variant disrupts a protein’s active site (e.g., enzymes or receptors), it’s more likely pathogenic. The ALK gene’s splice variants in lung cancer evade targeted therapies by altering the protein’s structure (1).
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Gain of Function: Rarely, splice variants create hyperactive proteins. In autoimmune diseases, aberrant PTPN2 splicing boosts inflammation by disabling a regulatory “brake” (6).
3. Experimental Validation
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RNA Analysis: Sequencing the mRNA confirms whether the variant causes abnormal splicing. For example, KCNQ1 splice variants in heart arrhythmias were confirmed by detecting unusual mRNA fragments in patient cells (10).
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Functional Tests: Lab-grown cells or animal models can show the variant’s impact. A SCN5A splice variant was shown to disrupt sodium channels in heart cells, validating its role in arrhythmias (10).
4. Population Data
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Frequency: Rare variants in healthy populations are less likely to be benign. The TERT gene’s splice variant is rare in the general population but common in melanoma and lung cancer patients (11).
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Disease Correlation: If a variant appears repeatedly in patients with a specific condition (e.g., OPN-c in breast cancer), it strengthens the case for pathogenicity (5, 8).
Why This Matters for Your Health
Understanding splice variants helps in:
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Diagnostics: Identifying harmful variants can guide cancer prognoses. Women with OPN-c-positive breast lesions have a 40% risk of cancer within 5 years vs. 10% for those without (5).
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Personalized Medicine: Drugs like lorlatinib target specific ALK splice variants in lung cancer, improving survival (1).
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Prevention: Genetic testing for splice variants in genes like CHEK2 can inform cancer screening schedules (9).
References
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Overcoming Central β-Sheet #6 (Cβ6) ALK Mutation (L1256F), TP53 Mutations and Short Forms of EML4-ALK v3/b and v5a/b Splice Variants are the Unmet Need That a Re-Imagined 5th-Generation (5G) ALK TKI Must Deliver (2024). NCBI. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10908247/
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PLP1-lacZ transgenic mice reveal that splice variants containing “human-specific” exons are relatively minor in comparison to the archetypal transcript and that an upstream regulatory element bolsters expression during early postnatal brain development (2023). NCBI. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9875078/
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Differential expression of interferon-lambda receptor 1 splice variants determines the magnitude of the antiviral response induced by interferon-lambda 3 in human immune cells (2020). NCBI. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217487/
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What’s Wrong in a Jump? Prediction and Validation of Splice Site Variants (2021). NCBI. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8482176/
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Osteopontin splice variants indicate prognosis in premalignant breast lesions (2023). Semantic Scholar. https://www.semanticscholar.org/paper/cceebc427448fe2063ac4c86928e48f0e63e92c8
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Low-usage splice junctions underpin immune-mediated disease risk (2023). Semantic Scholar. https://www.semanticscholar.org/paper/62a9f96beb931d091a4aaf837e55d48f14c00238
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FGD1 splice variants as predictors of brain and bone metastatic organotropism in clear cell renal cell carcinoma (2025). Semantic Scholar. https://www.semanticscholar.org/paper/6074368e6128ca2d3a484879d3f7b2a95522cfd7
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Breast cancer risk in premalignant lesions: osteopontin splice variants indicate prognosis (2018). NCBI. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251032/
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CHEK2 founder variants and thyroid cancer risk (2024). PubMed. https://pubmed.ncbi.nlm.nih.gov/38279823/
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Functional Assays Reclassify Suspected Splice-Altering Variants of Uncertain Significance in Mendelian Channelopathies. (2022). PubMed.
https://pubmed.ncbi.nlm.nih.gov/36197721/ -
Cumulative Evidence for Relationships Between Multiple Variants in the TERT and CLPTM1L Region and Risk of Cancer and Non-Cancer Disease. (2022). NCBI. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9279858/