rs234706 — CBS C699T

CBS C699T — A Protective Variant in the Transsulfuration Pathway

The CBS (cystathionine beta-synthase) gene encodes a critical enzyme that sits at the crossroads of [methylation | the process by which methyl groups are added to molecules, essential for DNA regulation, neurotransmitter production, and detoxification] and transsulfuration metabolism. CBS catalyzes the first step of the transsulfuration pathway, converting homocysteine¹¹ homocysteine
an amino acid that, when elevated, is associated with cardiovascular disease and inflammation into cystathionine, which ultimately becomes cysteine and glutathione — the body's master antioxidant. The [C699T variant | also known as rs234706 or p.Tyr233=, a synonymous change that does not alter the amino acid sequence] is one of the most studied CBS variants, yet remains controversial in the genetics community.

The Mechanism

rs234706 is a synonymous variant that does not change the amino acid at position 233 (tyrosine remains tyrosine) , yet individuals homozygous for the T allele show significantly reduced homocysteine-to-cystathionine ratios compared to heterozygous and wild-type individuals , suggesting altered CBS enzyme activity or expression. The mechanism remains debated: some believe the T allele leads to CBS upregulation and overproduction of ammonia or decreased glutathione, while most peer-reviewed publications find little to no evidence for negative effects .

The variant may influence CBS expression through effects on the non-coding RNA structure , even though it doesn't alter protein structure. CBS requires vitamin B6²² vitamin B6
in the form of pyridoxal-5-phosphate (P5P), the active cofactor for the enzyme and is allosterically activated by S-adenosylmethionine (SAMe), creating complex regulation within the methylation cycle.

The Evidence

The strongest evidence for rs234706 points to protective effects rather than harm.

A key study found TT homozygotes were significantly underrepresented in coronary artery disease patients (4.9% vs. 17.3% in controls), and these individuals showed the greatest response to folate supplementation, lowering homocysteine by 13.6% compared to 4.8% in CC homozygotes

³³ Kruger et al. Polymorphisms in the CBS Gene Associated with Decreased Risk of Coronary Artery Disease. Molecular Genetics and Metabolism, 2000.

The TT genotype was also associated with a halved risk of non-Hodgkin lymphoma (OR 0.51, 95% CI 0.31-0.84)

⁴⁴ Lim et al. Gene-Nutrient Interactions among Determinants of Folate and One-Carbon Metabolism on the Risk of Non-Hodgkin Lymphoma. Blood, 2007, suggesting the variant plays a protective role in cancer development. Additional research links the variant to improved LDL cholesterol and total cholesterol profiles, with liver samples showing significant CBS dysregulation in minor allele carriers .

The controversial "ammonia toxicity" theory — popularized in functional medicine circles — lacks support from studies measuring homocysteine levels, which have not shown the expected decreases that would indicate increased CBS activity .

Given the high prevalence of C699T heterozygosity (40-50% of populations), extreme dietary restrictions based on this variant alone are likely unwarranted unless ammonia testing confirms elevation .

Practical Implications

If you carry one or two copies of the T allele (A in dbSNP orientation), the evidence suggests you may have enhanced CBS pathway function, leading to more efficient homocysteine clearance — especially when folate intake is adequate. This translates to cardiovascular protection and reduced inflammation. The key is supporting the pathway with proper cofactors: vitamin B6 is essential for CBS function, and folate intake is particularly beneficial for T allele carriers .

The notion that CBS C699T carriers should avoid sulfur-containing foods (eggs, garlic, onions, cruciferous vegetables) stems from speculation about ammonia overproduction, but this is not well-supported by evidence. Some individuals with genuine sulfur sensitivity may benefit from dietary modifications, but this should be confirmed through biochemical testing (serum ammonia, urinary sulfates) rather than genetics alone.

Interactions

CBS sits at a critical juncture where the methylation and transsulfuration pathways intersect. Individuals with both MTHFR variants (rs1801133 C677T and rs1801131 A1298C) and CBS C699T may experience a balancing effect: reduced MTHFR activity causes homocysteine accumulation, while enhanced CBS activity (if present) helps clear it through the transsulfuration pathway . This gene-gene interaction can result in normal homocysteine levels despite MTHFR impairment, though it may increase demand for B vitamins.

The CBS variant's protective effects appear strongest when folate and vitamin B6 status are adequate, highlighting a gene-nutrient interaction. Other CBS variants (rs1801181 A360A) may compound effects on sulfur metabolism and should be considered in comprehensive methylation assessments.