NAT2 rs1799929: What Your Genotype Means
The rs1799929 variant is a specific genetic change within the NAT2 gene. While it does not change the protein structure itself, it serves as a key diagnostic marker used by researchers to identify haplotypes associated with the body's ability to process certain medications.
What each genotype means
Likely rapid or intermediate acetylator
You carry two reference copies of the C allele at this position, meaning you lack the defining silent tag for the NAT2*5 slow-acetylator haplotype cluster. Depending on other variants across your NAT2 gene, you are more likely to have normal or intermediate enzyme activity when processing drugs like isoniazid or hydralazine. If you are taking or considering medications metabolized by NAT2, discuss dosing and monitoring with your clinician or pharmacist.
Carried by approximately 30% to 40% of individuals of European ancestry and over 80% to 90% of individuals of East Asian ancestry.
Carrier of slow-acetylator tag
You carry one copy of the T allele, which serves as a diagnostic tag for the reduced-function NAT2*5 haplotype cluster. Individuals with this genotype typically exhibit an intermediate or slow acetylation phenotype depending on the haplotype inherited on the other chromosome. Because acetylation rates influence how quickly your body clears medications such as isoniazid or hydralazine, discuss your drug response and dosing with your healthcare provider.
Carried by roughly 45% to 50% of individuals of European descent, but less than 15% of individuals of East Asian ancestry.
Likely slow acetylator
You carry two copies of the T allele, which strongly tags homozygous inheritance of slow-acetylating haplotypes within the NAT2*5 cluster (such as NAT2*5/*5). This genetic profile is frequently associated with significantly slower clearance and higher exposure to medications like isoniazid, hydralazine, and certain sulfonamides, which can increase the likelihood of side effects. Consult your clinician or pharmacist to discuss medication selection and personalized dosing.
Carried by approximately 15% to 20% of European populations, but found in fewer than 1% to 2% of East Asian populations.
Understanding the rs1799929 Variant
The rs1799929 variant, also known as c.481C>T, is a single-nucleotide polymorphism (SNP) located within the coding region of the NAT2 gene. In genetics, this is often described as a synonymous or 'silent' mutation because the change from a cytosine (C) to a thymine (T) at this position does not alter the amino acid sequence of the resulting protein; it remains leucine. Despite this, rs1799929 is highly significant in pharmacogenomics. It is frequently used as a tag-SNP, meaning it is inherited in close proximity to other functional variants. By identifying the presence of this specific marker, scientists can reliably infer the presence of larger genetic patterns, or haplotypes, that do impact how the NAT2 enzyme functions in the body.
The Role of the NAT2 Gene
The NAT2 gene provides instructions for making an enzyme called N-acetyltransferase 2. This enzyme is primarily responsible for the phase II metabolism of various drugs and environmental toxins through a process called acetylation. The speed at which this enzyme works varies significantly between individuals, leading to classifications of 'rapid,' 'intermediate,' or 'slow' acetylators. Because the NAT2 enzyme is critical for breaking down medications like isoniazid—a common treatment for tuberculosis—an individual's acetylator status can influence how quickly these drugs are cleared from the bloodstream. Those who are slow acetylators may process these medications more slowly, which can lead to higher concentrations of the drug in the body and, in some clinical contexts, an increased risk of side effects such as liver toxicity.
Research and Clinical Associations
Research into NAT2 has primarily focused on its impact on drug safety, particularly regarding anti-tuberculosis therapy. Numerous studies have demonstrated that individuals classified as slow acetylators are at a higher risk of developing drug-induced liver injury when treated with isoniazid-based regimens. While rs1799929 itself is a silent mutation and does not directly cause the slow acetylator phenotype, it is a vital component of the multi-SNP panels used to predict this status. The evidence linking inferred slow acetylator status to hepatotoxicity is robust across various global populations. However, it is important to note that genetic status is only one factor in drug response. If you are concerned about how your genetics might influence your response to a specific medication, you should discuss this with your clinician or pharmacist, who can interpret these results in the context of your overall health.
Population Frequency
The frequency of the T allele at rs1799929 varies by ancestry. It is relatively common in European populations, with a minor allele frequency (MAF) typically ranging between 0.35 and 0.45. In contrast, the variant is less common in East Asian populations, where the MAF is generally observed between 0.05 and 0.10.
What This Information Means for You
Knowing your genotype for rs1799929 provides insight into your genetic makeup, but it is not a medical diagnosis. Because this variant is a marker for broader haplotypes, it is most useful when analyzed as part of a larger panel of NAT2 SNPs. This information is intended for educational purposes to help you understand the field of pharmacogenomics. It cannot predict your exact reaction to any medication, as factors like age, liver function, diet, and other concurrent medications also play significant roles. If you have received genetic testing results that include this variant, do not make any changes to your prescribed medications based on this information alone. Always consult with your healthcare provider to determine if pharmacogenomic testing is appropriate for your specific clinical situation.
How common is this variant?
The rs1799929 variant shows significant ancestral variation, with a minor allele frequency of approximately 0.35-0.45 in Europeans and 0.05-0.10 in East Asians.
Frequently asked questions
Is rs1799929 a cause of slow drug metabolism?
No, rs1799929 is a silent mutation that does not change the NAT2 protein. It is used as a genetic marker to identify other nearby changes that do affect the enzyme's speed.
Can I use this SNP to predict my risk of liver injury?
While NAT2 slow acetylator status is linked to liver injury risk from certain drugs, this single SNP is only one piece of the puzzle. You should never use genetic data to assess medical risk without professional clinical guidance.
What is a 'slow acetylator'?
A slow acetylator is someone whose NAT2 enzyme processes certain drugs more slowly than average. This can lead to higher drug levels in the blood, which may increase the risk of side effects.
Should I change my medication based on my NAT2 genotype?
Absolutely not. Never change your medication dosage or schedule based on genetic test results without consulting your doctor or pharmacist, as they must consider your full medical history.
Sources & further reading
Educational information only, last refreshed 10/28/2026. Not medical advice — these associations describe population statistics, not individual predictions.
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Coding variant c.857G>A (p.Gly286Glu) defining the NAT2*14 allele (often associated with slow acetylation).
Missense variant (590G>A) defining the NAT2*6A allele, associated with slow acetylator phenotype.
Synonymous polymorphism (857G>A) representing the defining mutation of the slow acetylator NAT2*7 allele.
Synonymous variant (282C>T) associated with the NAT2*6 allele, contributing to slow acetylator status.
This variant (c.590G>A, p.Arg197Gln) is a well-characterized slow acetylator allele in the NAT2 gene, influencing the metabolism of drugs like isoniazid.
Tag SNP defining the rapid versus slow N-acetyltransferase 2 acetylator phenotype, showing substantial allele frequency divergence across world ancestries.