rs5743810 — TLR6 Ser249Pro

Coding variant replacing serine with proline at TLR6 position 249, altering TLR2/TLR6 heterodimer signaling intensity for diacylated lipopeptides from bacteria and mycoplasma — Pro249 confers stronger NF-κB activation while Ser249 reduces TLR2/TLR6-mediated inflammation, with consequences for leprosy susceptibility, cardiovascular risk, and upper genital tract infections

See your personal result for TLR6

Upload your DNA data to find out which genotype you carry and what it means for you.

Upload your DNA data

Works with 23andMe, AncestryDNA, and other DNA test exports. Results in under 60 seconds.

TLR6 Ser249Pro — Tuning the Mycoplasma Alarm

Your immune cells face a daily challenge: detecting bacteria and mycoplasmas without triggering damaging inflammation. Toll-Like Receptor 6 (TLR6)11 Toll-Like Receptor 6 (TLR6)
a pattern-recognition receptor that pairs with TLR2 to detect diacylated lipopeptides — the molecular signature of mycoplasma cell membranes and some gram-positive bacteria is a front-line sensor calibrated for exactly this task. The rs5743810 Ser249Pro coding variant at position 249 of the extracellular domain alters how effectively TLR2/TLR6 heterodimers activate NF-κB upon encountering bacterial lipopeptides — setting a higher or lower inflammatory threshold that ripples through cardiovascular health, infection defense, and reproductive immunology.

TLR6 operates exclusively as an obligate heterodimer with TLR2. While TLR1/TLR2 heterodimers detect triacylated lipopeptides from mycobacteria and spirochetes, TLR2/TLR6 heterodimers are specialized for diacylated lipopeptides22 diacylated lipopeptides
lipoproteins with two fatty acid chains, the primary lipid motif of Mycoplasma species, Staphylococcus aureus lipoprotein MALP-2, and various gram-positive bacterial lipoteichoic acids — making TLR6 the gatekeeper for a distinct arm of bacterial recognition that TLR1 cannot substitute for.

The Mechanism

The Ser249Pro change substitutes serine (polar, hydroxyl side chain) with proline (rigid, cyclic imino acid) at position 249 in the extracellular leucine-rich repeat domain of TLR6. Unlike the TLR1 I602S variant — which prevents TLR1 from reaching the cell surface entirely — TLR6 Ser249Pro does not abolish surface expression. Instead, it modulates NF-κB activation efficiency33 NF-κB activation efficiency
the downstream transcriptional response that drives production of TNF-α, IL-6, IL-12, and other inflammatory cytokines when TLR2/TLR6 detects a diacylated lipopeptide.

Research in peripheral blood monocytes demonstrates the functional gradient directly: the G allele (Pro249) drives stronger NF-κB signal activation compared to the A allele (Ser249)44 the G allele (Pro249) drives stronger NF-κB signal activation compared to the A allele (Ser249)
differential TLR2/TLR6-mediated signaling has been confirmed in primary monocytes genotyped for this variant in response to TLR2/6 agonists. The result is a continuous inflammatory set-point dial: Pro/Pro homozygotes (GG) mount the most robust diacylated lipopeptide responses; Ser/Ser homozygotes (AA) operate at a lower baseline; heterozygotes (AG) fall in between.

The proline substitution itself likely reshapes the local tertiary structure of the extracellular domain, altering how TLR6 presents itself for dimerization with TLR2 and ligand coordination. TLR2/6 heterodimer signaling does not require endosomal maturation — it operates at the plasma membrane surface — so changes in extracellular domain geometry directly affect ligand binding kinetics and downstream signaling efficiency.

The Evidence

Leprosy provides the most thoroughly characterized association. A 2023 Colombian case-control study (Cardenas-Bedoya et al., 202355 Cardenas-Bedoya et al., 2023
114 leprosy cases and 456 controls, adjusted for age and sex) found sex-specific effects: in males, the A/G heterozygous genotype was protective in codominant (OR 0.37, 95% CI 0.16–0.86, p=0.049) and dominant models (OR 0.39, 95% CI 0.17–0.87, p=0.016), indicating that carrying even one Ser249 (A) allele — with its reduced TLR2/6 signaling — partially protects men against leprosy. In women, however, the CGG haplotype combining rs5743618 (TLR1 reduced surface expression), rs5743708 (TLR2 R753Q), and the G allele of rs5743810 was a susceptibility factor (OR 1.86, p=0.019), with particularly strong effects in the female subgroup (OR 2.39, p=0.013). This suggests that the combined effect of reduced TLR1/2/6 signaling across all three receptors creates a vulnerability to leprosy clinical disease in women through a different mechanism than the single-SNP effect in men.

Cardiovascular disease reveals the systemic cost of high TLR6 activity. A case-control study in Caucasians (1,118 participants, 513 CAD vs 605 controls66 1,118 participants, 513 CAD vs 605 controls
two independent cohorts with echocardiographic and coronary angiographic confirmation) found the Ser/Ser (AA) genotype was significantly protective against coronary artery disease (OR 0.69, 95% CI 0.51–0.95, p=0.02). Ser/Ser controls appeared more frequently (20.7%) than cases (15.4%), while Pro/Pro (GG) was overrepresented among CAD patients (36.5% vs 30.4%). Mechanistically, chronic low-grade TLR2/6-mediated NF-κB activation driven by Pro249 likely accelerates macrophage foam cell formation and plaque development through heightened responses to bacterial lipopeptides encountered during translocation from gut flora.

Hypertension and cardiac remodeling show an analogous sex-specific pattern to leprosy. Patel et al. 201077 Patel et al. 2010
443 hypertensive patients (266 women, 177 men) with echocardiography and cytokine measurements found that women homozygous for Ser249 (AA) had significantly lower LV posterior wall thickness (9.4 ± 0.4 vs. 10.5 ± 0.1 mm, p=0.02), interventricular septum thickness, and LV relative wall thickness than women with other genotypes. Their monocytes also produced less TNF-α and IL-6 in response to zymosan (a TLR2/6 agonist). No such difference appeared in men. The convergence of lower TLR2/6 inflammatory response and reduced cardiac remodeling specifically in Ser/Ser women supports a mechanism where chronic TLR2/6 activation by Pro249 drives pressure-volume remodeling in hypertensive hearts.

Pelvic inflammatory disease shows that the reduced signaling of Ser249 has organ-specific protective effects. Cherpes et al. 201388 Cherpes et al. 2013
racial variation study in PID patients found that African American women carrying the Ser249 (A, or coding-strand T) allele had significantly lower rates of endometritis and upper genital tract infection (OR 0.4, 95% CI 0.2–0.9, p=0.04). African American women were also 83% less likely than white women to carry any Ser249 alleles (OR 0.1, p<0.0001), reflecting the near-fixation of Pro249 (G allele) in African populations (>92%). The Ser249 allele likely reduces the TLR2/6-mediated inflammatory cascade triggered by ascending genital tract bacteria, limiting tissue damage and infection spread.

Atopy and allergic disease present a nuanced picture. The Hoffjan et al. 2005 study in 890 European subjects found a weak association between Ser249 (A allele) and childhood asthma (p=0.03), which did not survive Bonferroni correction. A subsequent bronchiolitis cohort found the A allele (Ser249) associated with atopic eczema and greater exercise-induced airway resistance at preschool age — consistent with reduced TLR2/6 signaling altering the Th1/Th2 balance toward atopy during early immune development.

Practical Implications

This variant operates as a dial on the TLR2/6 arm of innate immunity. The Pro249 (GG) genotype sets a higher inflammatory threshold — more protective initial bacterial sensing, but with chronic cardiovascular costs and some susceptibility to immunopathology from chronic infections like leprosy. The Ser249 (AA) genotype dampens this arm, reducing CAD and PID risk but potentially shifting atopic risk in early childhood and limiting certain mycobacterial defense pathways.

Globally, the G allele (Pro249) is the dominant form — near-fixed in East Asian and South Asian populations, and highly prevalent in Africans (92%). In Europeans, both alleles are common (Pro249 ~59%, Ser249 ~41%), making this population the most informative for heterozygous effects. Population-specific differences in Pro249 prevalence partially explain why associations with infection outcomes and CAD vary by ancestry in study populations.

Interactions

TLR6 works exclusively through TLR2 (rs5743708). The TLR2 R753Q variant independently impairs TLR2 signaling from the intracellular TIR domain side — so combining any TLR2 R753Q genotype with Ser249 TLR6 (A allele) compounds the reduction in diacylated lipopeptide recognition from two separate points: extracellular domain signaling efficiency (TLR6) and intracellular adaptor recruitment (TLR2). Conversely, the CGG haplotype (rs5743618-C / rs5743708-G / rs5743810-G) bundles reduced TLR1 surface expression with Pro249 TLR6 and wild-type TLR2 — and despite Pro249's stronger TLR6 signaling, the combined haplotype associates with leprosy susceptibility, suggesting that loss of TLR1-dependent signaling is the dominant driver of that risk.

TLR1 (rs5743618) handles the triacylated lipopeptide arm of diacylated-vs-triacylated bacterial lipopeptide recognition — its I602S variant selectively impairs TLR1/TLR2 without affecting TLR2/TLR6. Full innate bacterial immune profiling across TLR1, TLR2, and TLR6 provides the most complete picture of pattern-recognition receptor competence. TLR4 (rs4986790) handles gram-negative LPS independently of both heterodimer systems.

Genotype Interpretations

What each possible genotype means for this variant.

AG Intermediate TLR2/6 Signaling Intermediate

Ser249/Pro249 heterozygote — balanced TLR2/6 inflammatory response with moderate cardiovascular and infection implications

Heterozygotes produce a mixed TLR6 protein pool — some Ser249 TLR6 (lower NF-κB activation) and some Pro249 TLR6 (higher NF-κB activation) — resulting in an intermediate inflammatory response. This intermediate phenotype may be optimal in some settings: enough TLR2/6 activity for effective bacterial clearance, but not so much as to drive the chronic low-grade inflammation that accelerates atherosclerosis.

The leprosy finding is notable. In the Colombian cohort, it was the A/G heterozygote — not the AA homozygote — that showed the strongest protective signal in men. This may reflect heterozygote advantage: partial Ser249 expression reduces TLR2/6-driven immunopathology in M. leprae-infected nerves while preserving enough Pro249 signaling for initial pathogen recognition. This type of over-dominance is also documented for TLR2 R753Q heterozygotes.

For PID risk, you retain one Pro249 allele (higher TLR2/6 activity) but also one Ser249 allele that may modulate the inflammatory cascade in the upper genital tract.

AA Reduced TLR2/6 Signaling Decreased

Ser249 homozygote — lowest TLR2/6 inflammatory activity, associated with reduced cardiovascular risk

The Ser249 homozygous state produces the most muted NF-κB activation when TLR2/TLR6 heterodimers are engaged by diacylated bacterial lipopeptides. In monocyte studies, Ser249 cells release significantly less TNF-α and IL-6 in response to TLR2/6 agonists compared to Pro249 cells.

The cardiovascular benefit is the most consistently replicated finding: in a Caucasian case-control study of 1,118 participants, the Ser/Ser genotype was significantly overrepresented among healthy controls vs CAD patients (OR 0.69, p=0.02). In hypertensive women specifically, Ser/Ser was associated with lower LV posterior wall thickness and interventricular septum thickness — consistent with chronically reduced TLR2/6-driven macrophage activation limiting plaque and fibrotic remodeling.

This genotype is rare in populations with high leprosy burden (Sub-Saharan Africa, South Asia), where Pro249 is near-fixed. In leprosy-endemic contexts, the A/G heterozygous genotype — not the AA homozygous form — appears specifically protective in males, with AA data being sparse.

GG Elevated TLR2/6 Signaling High

Pro249 homozygote — strongest TLR2/6-mediated inflammatory response, associated with elevated cardiovascular risk

The Pro249 homozygous state maximizes TLR2/6 heterodimer activation efficiency. Proline at position 249 alters the extracellular domain structure of TLR6 in a way that increases NF-κB signal transduction when the receptor engages diacylated lipopeptides from bacteria and mycoplasma. This higher inflammatory set-point is likely the ancestral state in most human populations — it conferred strong early bacterial defense in environments with high microbial burden.

The cardiovascular association is the most robustly replicated finding: in a 1,118- person Caucasian case-control study, Pro/Pro individuals were significantly more likely to be CAD cases (36.5%) vs controls (30.4%), with overall Ser/Ser OR=0.69 (p=0.02). In hypertensive women specifically, non-Ser/Ser women (predominantly GG and AG) showed significantly greater LV wall thickness and higher TLR2/6-stimulated cytokine release — suggesting that chronic TLR2/6 activity under the hemodynamic stress of hypertension accelerates cardiac remodeling.

For leprosy, the GG genotype represents the highest-signaling form. The Colombian study found that in women, the CGG haplotype (which includes GG at rs5743810) was associated with leprosy susceptibility (OR 2.39), though this haplotype effect is driven by the combined context of all three TLR variants, not rs5743810 GG in isolation. For PID risk, GG women have the highest TLR2/6 inflammatory potential in the upper genital tract — the Ser249 A allele was specifically protective in African Americans where A is rare.

The near-fixation of Pro249 in African and East Asian populations suggests positive selection for strong TLR2/6 signaling in environments with high mycoplasma and bacterial burden historically. The cardiovascular cost of this advantage became apparent in the context of modern inflammatory triggers (dysbiosis, smoking, dietary lipids) and longer lifespans.