rs4570625 — TPH2 G-703T

The Brain's Serotonin Factory Switch

TPH2 (tryptophan hydroxylase 2) is the rate-limiting enzyme¹¹ rate-limiting enzyme
The slowest step in a biochemical pathway, which determines the overall speed of production for serotonin synthesis in the brain. Unlike its cousin TPH1, which makes serotonin in the gut and other peripheral tissues, TPH2 works exclusively in neurons—particularly in the raphe nuclei²² raphe nuclei
Clusters of serotonin-producing neurons in the brainstem that project throughout the brain, regulating mood, sleep, and emotional processing of the midbrain. The rs4570625 variant sits 703 base pairs upstream of the TPH2 gene's start site, in a regulatory region that controls how much enzyme gets made.

The Mechanism

This G>T substitution affects a promoter region where transcription factors³³ transcription factors
Proteins that bind to DNA and control gene expression by turning genes on or off bind to initiate TPH2 gene expression. In vitro studies suggest the T allele is associated with reduced TPH2 promoter activity, potentially lowering serotonin synthesis capacity. Brain imaging studies have found that carriers of different alleles show altered reactivity in the amygdala⁴⁴ amygdala
The brain's emotional processing center, especially for fear and threat detection and ventromedial prefrontal cortex⁵⁵ ventromedial prefrontal cortex
Brain region involved in emotional regulation, decision-making, and inhibiting negative emotions during emotional tasks.

The Evidence

The most comprehensive evidence comes from a 2012 meta-analysis of 27 studies including 13,041 cases and 11,568 controls, which found rs4570625 significantly associated with major depressive disorder (summary OR = 0.83, 95% CI: 0.73–0.96) . However, the direction of risk has been contentious.

A 2017 Estonian population study found that TT homozygous males reported less aggressive behavior, lower scores on maladaptive impulsivity, fewer ADHD symptoms, and lower rates of anxiety disorders compared to G-allele carriers .

Yet other research points in the opposite direction.

A 2023 pharmacological fMRI study found that specifically GG carriers experienced anxiogenic effects during acute tryptophan depletion (which transiently lowers serotonin), while TT carriers did not .

The G-allele has been suggested to relate to hypofunction of tryptophan hydroxylase and lower serotonin synthesis rates , though the functional implications remain incompletely understood.

The clearest pattern emerges when considering gene-environment interactions⁶⁶ gene-environment interactions
When genetic variants influence how a person responds to environmental factors like stress, creating different outcomes than either factor alone.

Single marker analyses showed significant gene-by-environment interactions with rs4570625 on depressive symptoms .

An interaction between TPH2 rs4570625 and BDNF Val66Met yields two at-risk groups for difficulty inhibiting negative emotional content: BDNF Val/Val combined with TPH2 G/G, and BDNF Met carriers combined with TPH2 T allele .

Practical Implications

Because the functional effects of this variant depend heavily on genetic background and environmental context, the practical guidance is less about the variant itself and more about understanding your vulnerability patterns. If you're a GG carrier, you may be more susceptible to mood changes when serotonin synthesis is temporarily compromised—for example, during periods of high stress, poor sleep, or low dietary tryptophan intake. TT carriers appear more resilient to transient serotonin fluctuations but may have other vulnerabilities depending on interactions with variants in genes like BDNF.

The key actionable insight is that serotonin synthesis depends on adequate tryptophan (the dietary precursor), cofactors like vitamin B6⁷⁷ vitamin B6
Required for the enzyme that converts 5-hydroxytryptophan to serotonin, and iron (required for TPH2 enzyme function). Unlike some genetic variants where supplementation directly addresses the problem, TPH2 variants don't create a specific nutrient deficiency—they affect the efficiency of the enzyme that uses those nutrients.

Interactions

The most well-documented interaction is with BDNF rs6265 (Val66Met). The combination of BDNF genotype and TPH2 rs4570625 genotype creates distinct emotional regulation profiles that neither variant predicts alone. Specifically, BDNF Val/Val + TPH2 GG shows impaired negative emotion inhibition, as does BDNF Met + TPH2 T-carrier status, suggesting epistasis⁸⁸ epistasis
When the effect of one gene variant depends on the presence of another gene variant between these serotonergic and neurotrophic pathways.

Within the TPH2 gene itself, rs4570625 is in linkage disequilibrium⁹⁹ linkage disequilibrium
When variants are inherited together more often than would be expected by chance, forming haplotype blocks with rs11178997, rs1386494, and rs7305115, forming haplotypes that collectively influence TPH2 expression and psychiatric risk more than any single variant.

For those interested in understanding their broader serotonergic genetics, variants in SLC6A4 (serotonin transporter), HTR1A and HTR2A (serotonin receptors), and MAOA (serotonin degradation) interact with TPH2 to shape overall serotonergic tone and psychiatric vulnerability.