rs35936514 — LHPP LHPP depression risk variant

Intronic/3'UTR variant in LHPP, a histidine phosphatase essential for stress resilience in the prefrontal cortex — the T allele is associated with increased risk for major depressive disorder, particularly following chronic stress

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The Prefrontal Phosphatase — When Stress Rewires the Brain

Most people associate depression with serotonin. LHPP tells a different story — one about a small enzyme in the prefrontal cortex that quietly prevents stress from reshaping your brain. When LHPP function is reduced, chronic stress finds an open door into the neural circuitry that governs mood, motivation, and resilience.

LHPP encodes phospholysine phosphohistidine inorganic pyrophosphate phosphatase11 phospholysine phosphohistidine inorganic pyrophosphate phosphatase
A HAD-family phosphatase that removes phosphate groups from histidine residues on target proteins. Histidine phosphorylation is an understudied but functionally important post-translational modification in mammalian cells, regulating kinase signaling cascades. It was essentially unknown in psychiatry until the CONVERGE consortium22 CONVERGE consortium
Collaborative Research on the Genetics of Depression in East Asians — a large-scale genetics consortium focused on recurrent major depressive disorder in Han Chinese women identified it in a landmark 2015 Nature study33 a landmark 2015 Nature study
CONVERGE consortium. Sparse whole-genome sequencing identifies two loci for major depressive disorder. Nature, 2015, sequencing 5,303 cases and 5,337 controls to find just two genome-wide significant loci — one near SIRT1 and one in LHPP (P = 6.45 × 10⁻¹²). The rs35936514 variant sits in the 3' UTR and flanking intronic region of LHPP on chromosome 10, likely affecting expression levels rather than protein structure.

The Mechanism

LHPP acts as a brake on stress-induced neuronal dysfunction. In the medial prefrontal cortex44 medial prefrontal cortex
A region of the prefrontal cortex critical for executive function, emotional regulation, and the top-down suppression of the stress response. It communicates extensively with the amygdala and hippocampus to modulate fear and mood (mPFC), LHPP dephosphorylates a network of histidine kinase substrates55 histidine kinase substrates
Proteins — including NME1/2 — that carry phosphate groups on histidine amino acids. When these kinases are over-active, downstream signaling cascades including MAPK and PI3K/AKT are altered, reducing glutamatergic synaptic transmission including NME1/2. When LHPP levels fall — whether from reduced expression due to the T allele or from chronic stress itself suppressing LHPP — histidine phosphorylation rises unchecked, weakening glutamatergic synaptic transmission in exactly the circuits that should be most resilient.

Lin et al. (2023)66 Lin et al. (2023)
Lin D et al. LHPP, a risk factor for major depressive disorder, regulates stress-induced depression-like behaviors through its histidine phosphatase activity. Molecular Psychiatry, 2023 showed in mice that mPFC LHPP deletion alone produced no spontaneous depression-like behavior — but on exposure to chronic social defeat stress, LHPP-knockout mice showed dramatically augmented behavioral deficits. Crucially, re-introducing wild-type LHPP reversed the deficits, while a phosphatase-dead LHPP mutant did not, confirming the enzymatic activity is required. A parallel mechanism runs through astrocytes: Sha et al. (2023)77 Sha et al. (2023)
Sha L et al. LHPP-mediated inorganic pyrophosphate hydrolysis-driven lysosomal acidification in astrocytes regulates adult neurogenesis. Cell Reports, 2023 showed that LHPP normally drives lysosomal acidification88 lysosomal acidification
Lysosomes require an acidic environment (pH ~5) to function as the cell's recycling centers. In astrocytes, LHPP hydrolyzes inorganic pyrophosphate to fuel this acidification. Without it, lysosomal function is impaired, the C/EBPβ transcription factor accumulates, and downstream chemokine signaling promoting neurogenesis is triggered in astrocytes; in its absence, the C/EBPβ pathway triggers compensatory adult neurogenesis that confers stress resilience. This counterintuitive finding (less LHPP → more resilience in knockout mice) may reflect that the full-knockout model removes a gene globally, while the rs35936514 T allele reduces rather than abolishes LHPP expression in specific circuits.

In the ventral hippocampus, a complementary mechanism operates: Zhuang et al. (2024)99 Zhuang et al. (2024)
Zhuang L et al. LHPP in glutamatergic neurons of the ventral hippocampus mediates depression-like behavior by dephosphorylating CaMKIIα and ERK. Biological Psychiatry, 2024 found that LHPP levels increase in glutamatergic neurons during stress-induced depression, and that knocking out LHPP in these neurons enhanced spontaneous activity and stress resilience via the CaMKIIα/ERK pathway1010 CaMKIIα/ERK pathway
CaMKII (calcium/calmodulin- dependent protein kinase II) and ERK (extracellular signal-regulated kinase) regulate synaptic plasticity and BDNF expression. LHPP dephosphorylates both, reducing their activity and impairing the BDNF/PSD95-mediated synaptic strengthening that underlies mood resilience. Esketamine — but not fluoxetine — reversed LHPP-induced depression-like behaviors, pointing toward glutamatergic rather than serotonergic modulation as the relevant therapeutic axis.

The Evidence

The CONVERGE study represents one of the cleanest GWAS findings in depression genetics. By restricting the sample to Han Chinese women with recurrent, severe MDD — reducing phenotypic and genetic heterogeneity — the consortium achieved genome-wide significance with just 10,640 individuals, far fewer than most psychiatric GWAS require. The LHPP signal (P = 6.45 × 10⁻¹²) was validated in an independent replication cohort. rs35936514 sits in intron 2 of LHPP and the flanking 3' UTR, and the T allele is associated with reduced LHPP expression in the prefrontal cortex.

At the neural circuit level, Cui et al. (2020)1111 Cui et al. (2020)
Cui L et al. Association of LHPP genetic variation (rs35936514) with structural and functional connectivity of hippocampal-corticolimbic neural circuitry. Brain Imaging and Behavior, 2020 examined 122 healthy participants and found that T-allele carriers showed increased hippocampal connectivity to the rostral anterior cingulate cortex and higher fractional anisotropy in the fornix — structural and functional signatures consistent with altered top-down emotional regulation. These brain connectivity differences were present without clinical depression, suggesting the risk phenotype is a continuous trait rather than a categorical diagnosis.

Earlier family-based work by Neff et al. (2009)1212 Neff et al. (2009)
Neff CD et al. Evidence for HTR1A and LHPP as interacting genetic risk factors in major depression. Molecular Psychiatry, 2009 found a chromosome 10 linkage peak (HLOD = 4.4) in Utah pedigrees with familial depression and identified disease-segregating LHPP SNPs in the linkage region. The LHPP effects in that study were contingent on HTR1A genotype, hinting at an interaction between serotonin receptor sensitivity and LHPP-mediated stress signaling.

Practical Implications

The LHPP mechanism converges on a clear biological theme: glutamatergic synaptic function under stress. T-allele carriers do not appear to have impaired mood at baseline — the risk emerges under chronic stress. This has direct implications for how carriers should think about their mental health strategy: minimizing the duration and intensity of chronic stressors matters more than managing acute stress reactions.

The esketamine finding from Zhuang et al. is clinically relevant: if depression does develop in T-allele carriers, the evidence points toward glutamate-targeting treatments (esketamine/ketamine) having particular mechanistic relevance versus standard SSRIs, which do not directly address the LHPP-CaMKII/ERK pathway.

Interactions

The Neff et al. (2009) data suggest a potential interaction between LHPP (rs35936514) and the HTR1A serotonin receptor gene. In that family-based study, the LHPP depression association was modulated by HTR1A genotype, suggesting that individuals carrying risk variants in both genes may have compounded vulnerability. The mechanistic intersection — serotonergic regulation of prefrontal excitatory tone — offers a plausible biological substrate.

The BDNF Val66Met variant (rs6265) is also relevant: since LHPP deficiency reduces CaMKII/ERK activity and thereby impairs BDNF/PSD95-mediated synaptic strengthening, T-allele carriers who also carry the BDNF Met allele (reduced activity-dependent BDNF secretion) may experience compounded vulnerability to stress-induced synaptic weakening in prefrontal and hippocampal circuits.

Genotype Interpretations

What each possible genotype means for this variant.

CC Standard Stress Resilience Normal

Common LHPP genotype — normal prefrontal stress resilience

The C/C genotype at rs35936514 is associated with normal LHPP expression in the medial prefrontal cortex and ventral hippocampus. LHPP at normal levels maintains controlled histidine phosphorylation of target proteins (including NME1/2), preserving glutamatergic synaptic transmission during stress. Astrocytic lysosomal acidification proceeds normally, supporting baseline adult neurogenesis. The CONVERGE GWAS and subsequent mechanistic studies consistently identify the T allele as the risk-associated variant; the C allele represents the ancestral, non-risk state at this locus.

CT Elevated Stress Vulnerability Intermediate

One copy of the depression risk allele — moderately increased vulnerability under chronic stress

Heterozygous CT carriers have one copy of the T allele, which reduces LHPP expression relative to CC homozygotes. This partial reduction in LHPP activity likely produces an intermediate phenotype: glutamatergic transmission and prefrontal-hippocampal connectivity are altered (as shown by Cui et al. 2020 in healthy T-allele carriers), but the clinical depression risk emerges primarily when the reduced enzymatic capacity is overwhelmed by chronic stress. The CaMKII/ERK pathway shows intermediate dephosphorylation efficiency, and BDNF/PSD95 expression at synapses may be marginally reduced under stress loads. The T allele frequency in East Asian populations is approximately 27-32%, meaning this genotype is considerably more common in those ancestries (projected CT + TT frequency: ~45-55% vs ~13% in Europeans).

TT High Depression Risk High Risk

Two copies of the LHPP depression risk allele — substantially elevated vulnerability under chronic stress

TT homozygotes at rs35936514 carry the greatest reduction in LHPP expression. Both copies of the gene's regulatory region carry the T allele, leading to the most impaired histidine phosphatase activity in the mPFC and ventral hippocampus under stress conditions. The CaMKIIα and ERK pathways remain over-phosphorylated during stress, impairing BDNF and PSD95 expression and weakening glutamatergic synaptic strength in circuits critical to mood regulation.

The brain imaging data from Cui et al. (2020) showed that T-allele carriers already exhibit altered hippocampal-rACC connectivity at rest, even without clinical depression — suggesting the neural signature of vulnerability is present before any mood episode. In terms of treatment, the Zhuang et al. (2024) Biological Psychiatry findings are directly relevant: esketamine (an NMDA receptor antagonist acting on the glutamate system) reversed LHPP-mediated depression-like behaviors in preclinical models, while fluoxetine (SSRI) did not. This mechanistic specificity may translate to better treatment outcomes with glutamate-targeting interventions if depression develops.

The T allele also carries a human mutation-level implication: human LHPP mutations E56K and S57L (identified in Zhuang et al. 2024) heightened CaMKII/ERK pathway signaling, confirming that even partial loss of LHPP function through natural variation is biologically meaningful.