KLK3 rs116940348: Understanding PSA Levels and Genetic Variation
The rs116940348 variant is a single-nucleotide polymorphism located within the KLK3 gene, which encodes prostate-specific antigen (PSA). Research suggests this variant is associated with variations in baseline PSA levels, which can influence how clinicians interpret prostate cancer screening results.
What each genotype means
Typical PSA baseline
This genotype represents the most common genetic configuration at this position in many populations. Research suggests this variant is associated with baseline prostate-specific antigen (PSA) levels, which are used in prostate cancer screening. Because PSA levels are influenced by many factors including age and prostate health, this genetic result should be interpreted by a clinician in the context of your overall medical history.
This is the most frequent genotype in populations of European ancestry.
Varied PSA baseline
Carrying one copy of the minor allele may be associated with slight differences in baseline prostate-specific antigen (PSA) levels compared to the common genotype. These associations are statistical in nature and do not indicate a diagnosis of any condition. Please discuss your PSA screening results and any concerns about prostate health with your healthcare provider.
Carried by roughly 1 in 10 to 1 in 20 people of European ancestry, based on a minor allele frequency of approximately 0.02 to 0.05.
Potential PSA baseline shift
This genotype is the least common and may be associated with altered baseline prostate-specific antigen (PSA) levels. While genetic variants in the KLK3 gene can influence PSA measurements, these levels are also significantly affected by non-genetic factors like prostate volume and inflammation. This information is for educational purposes and should not replace professional medical advice regarding prostate cancer screening.
This genotype is rare, occurring in less than 1% of individuals of European ancestry.
What is rs116940348?
The rs116940348 variant is a specific genetic change, or single-nucleotide polymorphism (SNP), found within the KLK3 gene. In genetics, a SNP represents a variation at a single position in the DNA sequence among individuals. This particular variant is located in the region of the genome responsible for the production of prostate-specific antigen (PSA). Because PSA is a protein widely used as a biomarker in clinical settings to screen for prostate health, variations in the gene that produces it are of significant interest to researchers. By studying how this specific SNP alters the genetic code, scientists aim to understand why baseline PSA levels can differ naturally between healthy individuals, independent of disease status.
The Role of the KLK3 Gene
The KLK3 gene provides instructions for making a protein called kallikrein-related peptidase 3, more commonly known as prostate-specific antigen (PSA). PSA is a serine protease, an enzyme that breaks down other proteins, and it is primarily synthesized in the epithelial cells of the prostate gland. Its main physiological function involves the liquefaction of seminal coagulum by cleaving proteins like semenogelin. While PSA is essential for reproductive health, it is most famous in medicine for its role as a screening tool. Because PSA is secreted into the bloodstream, clinicians measure its concentration to monitor prostate health. Genetic variants in KLK3 can influence the amount of PSA an individual produces, which is a critical factor when interpreting screening results.
Research and Evidence Strength
Current research into rs116940348 indicates that it is associated with altered baseline PSA levels. The evidence for this association is considered limited, meaning that while studies have observed a statistical link, the clinical implications are still being defined. A major challenge in this field is distinguishing between a true genetic risk for prostate cancer and 'detection bias.' If a genetic variant causes a person to have naturally higher or lower PSA levels, it may lead to more or fewer biopsies, respectively, regardless of the actual presence of cancer. Studies have shown that some KLK3 variants correlate with both PSA levels and prostate cancer risk, but it remains unclear if these variants are direct drivers of cancer or simply markers that influence the screening process itself.
Population Frequency
Genetic studies indicate that the rs116940348 variant is most frequently observed in populations of European ancestry. The minor allele frequency (MAF) for this variant typically ranges between 0.02 and 0.05 in these groups. This means that while the variant is present, it is not the most common form of the gene in the general population. Frequency data is essential for researchers to understand how genetic diversity impacts health outcomes across different ethnic groups. Because many large-scale genomic studies have historically focused on European cohorts, there is a need for more diverse research to determine if the associations observed with rs116940348 hold true across other global populations.
What This Information Means for You
It is important to understand that having a specific genotype for rs116940348 does not constitute a medical diagnosis. This variant is a tool for researchers to understand biological variability, not a definitive predictor of prostate cancer. If you are concerned about your PSA levels or prostate health, the most important step is to consult with a healthcare professional, such as a urologist or primary care physician. They can interpret your PSA results in the context of your overall health, family history, and other clinical factors. Never use genetic information to make decisions about screening or medical treatment without professional guidance. Genetic associations are statistical observations across large groups and cannot predict the health trajectory of any single individual.
How common is this variant?
The rs116940348 variant has a minor allele frequency of approximately 0.02 to 0.05 in populations of European ancestry.
Frequently asked questions
Does this variant mean I have prostate cancer?
No. This variant is associated with baseline PSA levels, which are used in screening, but it is not a diagnostic marker for prostate cancer. A genetic association is a statistical observation and does not determine your personal health status.
Should I get tested for this SNP?
There is currently no clinical recommendation to test for this specific SNP. PSA screening decisions should be based on clinical guidelines, your age, and discussions with your doctor, rather than individual genetic variants.
How does KLK3 affect PSA levels?
The KLK3 gene encodes the PSA protein. Genetic variations in this gene can influence how much PSA is produced or secreted, which can lead to natural variations in blood PSA levels between healthy individuals.
What is the difference between a risk variant and a screening marker?
A risk variant directly contributes to the biological development of a disease. A screening marker, like those in KLK3, may influence the test results used to detect a disease, potentially leading to detection bias.
Sources & further reading
Educational information only, last refreshed 10/16/2026. Not medical advice — these associations describe population statistics, not individual predictions.
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