SLC6A20 rs113899790: Understanding the 3p21.31 COVID-19 Risk Locus
The variant rs113899790 is a genetic marker located within the 3p21.31 gene cluster on chromosome 3. It has been identified in genome-wide association studies as being linked to an increased risk of developing severe respiratory failure when infected with COVID-19.
What each genotype means
Typical genetic risk profile
This genotype represents the most common genetic sequence found at this location in the SLC6A20 gene. Research into the 3p21.31 locus suggests that individuals with this sequence do not carry the specific genetic marker associated with increased susceptibility to severe COVID-19 respiratory failure. This finding is based on limited evidence and should not be used to predict individual health outcomes.
This is the most common genotype in most global populations, particularly in those of African and East Asian ancestry.
Increased risk marker present
Carrying one copy of the G allele at this position has been identified in large-scale studies as part of a risk haplotype on chromosome 3p21.31. While this variant is statistically associated with a higher risk of severe COVID-19 respiratory failure, the evidence remains limited and the clinical impact for any single individual is not well-defined. This association is most frequently observed in populations of European ancestry.
Carried by approximately 15% of individuals of European ancestry, while being significantly rarer in East Asian and African populations.
Elevated risk marker present
This genotype includes two copies of the G allele, which is part of a genetic cluster on chromosome 3p21.31 linked to severe COVID-19 respiratory failure in some studies. The association is considered to have limited evidence, and it is important to note that genetic risk is only one of many factors influencing health outcomes. You should discuss any concerns regarding respiratory health or infection risk with your healthcare provider.
This genotype is found in approximately 0.6% to 1% of individuals of European ancestry and is extremely rare in other global populations.
What is the rs113899790 Variant?
The rs113899790 variant is a single nucleotide polymorphism (SNP) situated in a region of the human genome known as 3p21.31. This specific chromosomal location has gained significant scientific attention due to its role as a susceptibility locus for severe outcomes following SARS-CoV-2 infection. A SNP represents a variation at a single position in the DNA sequence among individuals. While most SNPs have no observable effect on health, researchers study them to understand how specific genetic architectures might influence biological responses to environmental stressors, such as viral pathogens. The 3p21.31 region is complex, containing several genes that are involved in immune response and cellular function, making it a focal point for ongoing research into why individuals experience vastly different clinical outcomes when exposed to the same virus.
The Role of the SLC6A20 Gene
The SLC6A20 gene, which sits within the 3p21.31 locus, encodes a protein that functions as a proline transporter. This protein is known to interact with ACE2, the primary receptor that SARS-CoV-2 uses to enter human cells. Because of this functional relationship, scientists have hypothesized that variations in or near the SLC6A20 gene might influence the efficiency of viral entry or the subsequent inflammatory response in the lungs. Research suggests that the genetic signals in this region may modulate the expression of SLC6A20, potentially altering how cells manage proline transport or interact with the ACE2 receptor. While the exact biological mechanism remains a subject of active investigation, the proximity of this gene to the COVID-19 association signal makes it a primary candidate for explaining the observed clinical differences in respiratory severity.
Research and Evidence Strength
The association between the 3p21.31 locus and severe COVID-19 was first highlighted by large-scale genome-wide association studies (GWAS) during the early stages of the pandemic. These studies compared the genetic profiles of patients with severe respiratory failure against those with milder symptoms or healthy controls. While the statistical signal at this locus is robust and has been replicated across multiple cohorts, the evidence regarding the specific contribution of rs113899790 remains limited in terms of clinical utility. It is important to note that genetic associations are statistical correlations, not deterministic predictions. Having a specific genotype at this locus does not guarantee a particular health outcome, as COVID-19 severity is influenced by a multitude of factors, including age, underlying health conditions, vaccination status, and environmental exposure. Current research continues to bridge the gap between these correlational findings and a complete understanding of the underlying biological causality.
Population Frequency
The frequency of the rs113899790 variant varies significantly across different ancestral groups. In European populations, the variant is observed with a frequency of approximately 0.08. It is notably rarer in East Asian and African populations. These differences in allele frequency are common in human genetics and reflect the diverse evolutionary histories of global populations. Because the variant is more prevalent in some groups than others, researchers must account for ancestry when conducting association studies to ensure that findings are accurate and not confounded by population structure. Understanding these frequency distributions is essential for global health research, as it helps scientists determine whether genetic risk factors identified in one population are applicable to others.
What This Information Means for You
Information about genetic variants like rs113899790 is intended for educational and research purposes only. It is not a diagnostic tool and cannot be used to predict your personal risk of severe illness or to guide medical treatment. Genetic associations are complex and represent only a small fraction of the factors that determine health outcomes. If you have concerns about your health, your risk of infection, or how to manage your medical care, you should always consult with a qualified healthcare professional. They can provide personalized advice based on your complete medical history, current health status, and established clinical guidelines. Never make changes to your health regimen or medication based on information found in genetic databases or research articles without first discussing it with your doctor or pharmacist.
How common is this variant?
The variant has a frequency of approximately 0.08 in European populations, while it is significantly rarer in East Asian and African populations.
Frequently asked questions
Does having this variant mean I will get severe COVID-19?
No. Genetic associations are statistical findings across large groups and do not predict individual outcomes. Many factors, including age and overall health, play a much larger role in determining how your body responds to a virus.
Can I get tested for this variant to assess my risk?
While some direct-to-consumer tests may include this SNP, it is not a clinically validated test for COVID-19 risk. Medical professionals do not use this information to make clinical decisions or provide personalized risk assessments.
Is the SLC6A20 gene the only factor in COVID-19 severity?
Absolutely not. COVID-19 severity is multifactorial, involving the immune system, pre-existing health conditions, and environmental factors. The 3p21.31 locus is just one of many genetic regions that have been studied in relation to the disease.
What should I do if I know my genotype for this variant?
You should continue to follow public health guidelines and advice from your healthcare provider regarding COVID-19 prevention and care. Knowing your genotype for this specific SNP does not change standard medical recommendations.
Sources & further reading
Educational information only, last refreshed 9/17/2026. Not medical advice — these associations describe population statistics, not individual predictions.
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