rs13154066 — NPR3

Regulatory variant near the NPR3 natriuretic peptide clearance receptor gene associated with gestational hypertension and preeclampsia risk; the C allele may increase NPR3-mediated peptide clearance, impairing vasodilatory natriuretic signaling during pregnancy

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NPR3 — When Pregnancy's Pressure Safety Valve Fails to Open

Under normal circumstances, pregnancy is one of the most vasodilatory states the human body can enter. Cardiac output rises by 40–50%, systemic vascular resistance falls, and blood pressure drops in the first trimester before gradually returning toward pre-pregnancy levels at term. Several molecular systems drive this extraordinary expansion of vascular capacity — and natriuretic peptides are among the most important. Atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), and C-type natriuretic peptide (CNP) all promote vasodilation, suppress the renin-angiotensin-aldosterone system, and facilitate sodium excretion. But a gene variant near NPR3 — the receptor that silently removes all three peptides from circulation — may blunt this protective effect precisely when it is needed most.

The Mechanism

The NPR3 gene11 NPR3 gene
Natriuretic peptide receptor 3, also called NPR-C; located at chromosome 5p13.3; functions as a clearance receptor that binds ANP, BNP, and CNP with high affinity and removes them from circulation via receptor-mediated internalization and degradation encodes the dominant clearance mechanism for all three natriuretic peptides. Unlike NPR1 and NPR2 — which signal through intracellular guanylyl cyclase activity — NPR3 primarily acts as a "molecular sink," binding natriuretic peptides and internalizing them for degradation. When NPR3 is more highly expressed or more active, natriuretic peptides are cleared faster, their circulating half-life shortens, and their vasodilatory effects are attenuated.

The rs13154066 variant lies in a regulatory region approximately 40 kb upstream of the NPR3 transcription start site. Analogous blood pressure-associated NPR3 locus SNPs22 blood pressure-associated NPR3 locus SNPs
As shown for the rs1173771 block — blood pressure-elevating alleles reduce NPR3 mRNA in vascular smooth muscle cells via altered chromatin accessibility (Leach et al., Hum Mol Genet 2017, PMID 29016846) have been shown to modulate NPR3 transcript levels: alleles that increase blood pressure correspond to reduced NPR3 expression in vascular smooth muscle, but this apparently paradoxical finding reflects the complexity of the clearance receptor system — reduced NPR3-mediated clearance increases natriuretic peptide half-life, and its net effect on blood pressure can depend on which target tissue and which natriuretic peptide dominate in a given physiologic context. In pregnancy, the relevant signaling context shifts substantially: CNP acts on uterine smooth muscle and spiral arteries33 CNP acts on uterine smooth muscle and spiral arteries
CNP stimulates endometrial decidualization, promotes trophoblast invasion, and mediates spiral artery remodeling via NPR2 signaling that is tightly regulated by NPR3-mediated clearance, and impaired CNP signaling is mechanistically linked to defective spiral artery remodeling — a central pathologic feature of preeclampsia.

Direct molecular evidence links NPR3 dysregulation to preeclampsia: one study found that NPR-A was absent and NPR-C was upregulated in maternal vessel endothelium from preeclamptic women44 NPR-A was absent and NPR-C was upregulated in maternal vessel endothelium from preeclamptic women
Compared to normotensive pregnancies where NPR-C was undetectable in maternal vessels; n=12 tissue samples (6 preeclamptic, 6 normotensive) (Gu et al., Pregnancy Hypertens 2018, PMID 29523263), suggesting that in preeclampsia the balance tips toward clearance and away from productive natriuretic peptide signaling — precisely the opposite of what is needed for blood pressure control during pregnancy.

The Evidence

The strongest evidence for this SNP comes from a landmark multi-ancestry genome-wide association study of hypertensive disorders of pregnancy55 multi-ancestry genome-wide association study of hypertensive disorders of pregnancy
Honigberg et al., Nature Medicine 2023; tested 20,064 preeclampsia cases and 703,117 controls, and 11,027 gestational hypertension cases and 412,788 controls; multi-ancestry discovery and replication cohorts that identified rs13154066 as the lead variant at a new locus (5p13) specifically associated with gestational hypertension. Each additional C allele was associated with an approximately 11% higher odds of gestational hypertension (OR 1.11, p=4.5×10⁻¹⁰). Colocalization analysis and polygenic priority scores in this study independently nominated NPR3 as the most likely causal gene at this locus — not a nearby bystander gene.

The causal direction was confirmed in a two-sample Mendelian randomization66 two-sample Mendelian randomization
Harpe et al. Int J Hypertension 2025; used 12 NPR3 SNPs as instruments from female-specific UK Biobank data (n=198,402); outcome from 296,824-person preeclampsia GWAS: genetically proxied reduced NPR3 function was associated with a 54% lower odds of preeclampsia (OR 0.46, 95% CI 0.30–0.69). Because reduced NPR3 function means slower natriuretic peptide clearance and therefore higher circulating ANP/BNP/CNP levels, this finding is consistent with the hypothesis that natriuretic peptide signaling is protective in pregnancy hypertension.

A NPR3 missense variant rs2270915 (N521D) has been separately associated with diastolic dysfunction (OR 1.94, p=0.03) in 1,931 randomly selected adults77 diastolic dysfunction (OR 1.94, p=0.03) in 1,931 randomly selected adults
Pereira et al., PLOS ONE 2014; G/G homozygotes showed 43% diastolic dysfunction prevalence vs 28% in A/A+A/G genotypes and with blood pressure in two independent diabetic cohorts88 blood pressure in two independent diabetic cohorts
Saulnier et al., Diabetes Care 2011; AA homozygotes had ~2.5 mmHg lower SBP than G carriers and greater reduction with dietary salt restriction. These functional associations reinforce that NPR3 genetic variation has real physiologic consequences for cardiovascular regulation — and by extension, for the cardiovascular demands of pregnancy.

Practical Implications

Carriers of the CC genotype at rs13154066 may have modestly higher NPR3-driven natriuretic peptide clearance, attenuating the vasodilatory protection these peptides normally provide during pregnancy. The variant is common (~60% C allele frequency globally), meaning the vast majority of the population carries at least one C allele — its population impact on gestational hypertension risk is therefore substantial even though the per-person OR of 1.11 is modest.

For carriers of CT or CC genotypes, the actionable focus centers on blood pressure surveillance during pregnancy and awareness of gestational hypertension symptoms. Where natriuretic peptide signaling is relevant to clinical decision-making — such as in interpreting BNP or NT-proBNP levels — this genotype may provide useful context. The variant does not currently trigger changes in standard preeclampsia prevention protocols (low-dose aspirin is recommended based on clinical risk factors), but knowing one's genotype can inform both personal vigilance and conversations with prenatal care providers.

Interactions

PLCE1 rs932764 (phospholipase C epsilon 1): Both NPR3 rs13154066 and PLCE1 rs932764 were identified as independent preeclampsia-associated loci in the same Honigberg 2023 multi-ancestry GWAS, and PLCE1 was additionally identified in the multitrait analysis. NPR3 disrupts natriuretic peptide clearance (a blood pressure and vascular tone pathway), while PLCE1 mutations cause nephrotic syndrome and affect podocyte integrity and glomerular filtration — a second pathway that converges on the proteinuria-hypertension axis central to preeclampsia. Individuals carrying risk alleles at both loci may have dual vulnerability: impaired vasodilatory signaling from the NPR3 side and glomerular dysfunction susceptibility from the PLCE1 side, representing two independent pathophysiologic routes to the same clinical syndrome. Proposed compound action: rs13154066 CC + rs932764 risk genotype — "Dual Preeclampsia Risk: NPR3-Mediated Vascular and PLCE1-Mediated Renal Vulnerability." Action type: monitoring. Evidence level: moderate.

NPR3 rs2270915 (N521D missense): This separate NPR3 coding variant is associated with diastolic dysfunction and blood pressure, providing a functional layer of NPR3 impairment that compounds the regulatory effect of rs13154066. Individuals carrying risk alleles at both NPR3 loci (the GWAS regulatory variant and the N521D coding variant) may experience additive impairment of natriuretic peptide clearance efficiency and cardiac pressure-volume regulation. These two variants are in the same gene but appear to operate through distinct mechanisms (regulatory expression vs. protein function), and their combined effect on pregnancy blood pressure has not been formally studied.

Genotype Interpretations

What each possible genotype means for this variant.

TT Reduced Clearance Beneficial

Two T alleles — lower natriuretic peptide clearance, protective toward gestational blood pressure

You carry two copies of the T allele at rs13154066 near NPR3. The T allele appears to be associated with reduced expression or activity of the NPR3 natriuretic peptide clearance receptor, allowing ANP, BNP, and CNP to persist longer in circulation and exert their vasodilatory effects more fully. About 16% of the population carries this genotype, making it the least common of the three.

In the large multi-ancestry gestational hypertension GWAS (n>400,000), the T allele was inversely associated with gestational hypertension risk — TT homozygotes carry a modestly lower risk than CT or CC individuals. Mendelian randomization evidence supports the mechanistic direction: genetically proxied reduced NPR3 function (the T-allele direction) is associated with a 54% lower odds of preeclampsia.

CT Intermediate Clearance Intermediate

One C allele — modestly elevated gestational hypertension susceptibility

The OR 1.11 per allele from Honigberg et al. 2023 applies across the additive model for the entire cohort (cases from European, Asian, and African ancestries). In a heterozygous CT carrier, the individual contribution of this locus to gestational hypertension risk is modest, but it occurs against the background of all other known risk factors for preeclampsia: nulliparity, chronic hypertension, obesity, diabetes, multi-fetal pregnancy, prior preeclampsia, and autoimmune conditions. The NPR3 signal operates specifically through natriuretic peptide biology, distinct from the angiogenic (sFlt-1/PlGF) and trophoblast invasion pathways that dominate other preeclampsia risk loci.

Practically, CT individuals should be aware that their natriuretic peptide signaling may be mildly attenuated during pregnancy, and that blood pressure surveillance during the second and third trimesters is especially important.

CC Elevated Clearance High Risk

Two C alleles — highest NPR3-associated gestational hypertension susceptibility

CC homozygosity at this locus combines:

  1. The full additive OR for gestational hypertension (~1.23 for CC vs TT, based on two copies of the per-allele OR 1.11)
  2. A biological mechanism — NPR3-mediated natriuretic peptide clearance — that is mechanistically distinct from and potentially additive with other preeclampsia pathways (angiogenic imbalance, renin-angiotensin activation, placental trophoblast dysfunction)

In direct tissue studies, NPR3 upregulation was observed in maternal vascular endothelium from preeclamptic women (vs undetectable in normotensive pregnancies), supporting the idea that higher NPR3 activity represents a real pathophysiologic feature of preeclampsia rather than an epiphenomenon.

The absolute excess risk at this single locus remains moderate — the population frequency of CC is ~36% and gestational hypertension occurs in only 6–8% of pregnancies overall, so the vast majority of CC individuals will have uncomplicated pregnancies. However, the CC genotype should be treated as an additional motivator to optimize controllable risk factors and pursue diligent blood pressure monitoring.