rs35929607 — STK39

Intronic variant in the SPAK kinase gene that has been studied for association with blood pressure regulation through the WNK-SPAK-NCC sodium reabsorption axis

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STK39 (SPAK): The Kidney's Salt Volume Knob

Your kidneys handle roughly 25,000 mmol of sodium every day. How much stays in your body — and how much is excreted — is one of the most important determinants of blood pressure. The STK39 gene encodes SPAK (STE20/SPS1-related proline-alanine-rich kinase)11 SPAK (STE20/SPS1-related proline-alanine-rich kinase)
SPAK = serine/threonine kinase 39, a proximal effector of the WNK kinase hypertension pathway, a kinase that sits at the center of this sodium-handling circuit. rs35929607 is an intronic variant within STK39 that has been studied as a potential modifier of this system — though the evidence for its independent clinical effect is modest and population-dependent.

The Mechanism

The WNK-SPAK-NCC signaling cascade22 WNK-SPAK-NCC signaling cascade
WNK = With-No-Lysine kinase; NCC = sodium-chloride cotransporter (SLC12A3), the same transporter targeted by thiazide diuretics is one of the most clinically validated pathways in hypertension biology. The sequence works as follows: WNK1 and WNK4 kinases sense osmotic status and chloride concentration in the distal convoluted tubule of the kidney. When activated, WNK kinases phosphorylate SPAK at two key residues (T233 and S373), switching SPAK into its active conformation. Active SPAK then phosphorylates NCC (the thiazide-sensitive sodium-chloride cotransporter), increasing its surface expression and sodium reabsorption capacity. More SPAK activity means more NaCl retained, more plasma volume, and higher blood pressure.

The rs35929607 variant lies within an intron of STK39 and does not change the SPAK protein sequence. However, intronic variants can influence gene expression, splicing efficiency, or regulatory element activity. Cunnington et al. demonstrated that STK39 variants show significant cis-acting effects on SPAK expression in peripheral blood33 Cunnington et al. demonstrated that STK39 variants show significant cis-acting effects on SPAK expression in peripheral blood
13% overexpression associated with certain alleles, P=9.9×10⁻⁴, suggesting the locus regulates how much SPAK protein the cell produces, even without changing its structure. Higher SPAK expression would be expected to amplify NCC phosphorylation and sodium retention.

The biological plausibility of the STK39 locus is reinforced by mouse genetics: SPAK knockin mice engineered so that SPAK cannot be phosphorylated by WNK kinases showed significantly reduced blood pressure that was salt-sensitive44 SPAK knockin mice engineered so that SPAK cannot be phosphorylated by WNK kinases showed significantly reduced blood pressure that was salt-sensitive
blood pressure normalized on low-salt diet, confirming pathway specificity. SPAK inhibitors have since been proposed as a novel antihypertensive drug class, acting upstream of NCC — essentially mimicking the effect of thiazide diuretics at a higher point in the pathway.

The Evidence

The rs35929607 variant was identified in the original GWAS that established STK39 as a hypertension susceptibility locus. Wang et al. (2009) performed a whole-genome association study in an Amish cohort (n=542 discovery) followed by meta-analysis across 7,125 participants55 Wang et al. (2009) performed a whole-genome association study in an Amish cohort (n=542 discovery) followed by meta-analysis across 7,125 participants
Populations included Amish, Framingham Heart Study, Diabetes Genetics Initiative, GenNet, and Hutterites, identifying STK39 intronic variants associated with systolic blood pressure changes of 3.3 mmHg and diastolic changes of 1.3 mmHg (P<10⁻⁶ in meta-analysis).

However, replication has been inconsistent. A meta-analysis by Yang et al. (2016) pooling 9 studies found rs35929607 had OR=0.95 with p=0.507 — no significant association with hypertension66 A meta-analysis by Yang et al. (2016) pooling 9 studies found rs35929607 had OR=0.95 with p=0.507 — no significant association with hypertension
Substantial heterogeneity I²>80% across populations limits pooled estimates. Similarly, no association was detected in a British Caucasian family study (PMID 20003416) or in Chinese (PMID 23151749) or Iranian (PMID 30159265) populations.

The most consistent finding from population studies is that rs35929607 contributes to hypertension risk through epistatic interaction with other STK39 variants rather than independently77 epistatic interaction with other STK39 variants rather than independently
A three-SNP model including rs35929607, rs6749447, and rs3754777 achieved 73% prediction accuracy for hypertension in Chinese northeastern Han (n=1,765). In a Pakistani cohort, the G allele was nominally associated with 3.07 mmHg higher blood pressure per allele (p=0.001), but the effect was dwarfed by environmental factors (age, BMI, diabetes — conferring a 12-fold risk in GG carriers). A Belgian cohort found that the neighboring rs3754777 TT genotype carried OR=5.9 for hypertension, suggesting allelic heterogeneity within this locus.

Practical Actions

For individuals carrying one or two G alleles, the actionable implication is not genetic determinism but elevated salt sensitivity. The WNK-SPAK-NCC axis is the principal molecular target of thiazide diuretics — the most widely prescribed antihypertensive drug class. Any variant affecting SPAK expression or activity influences the same renal sodium-handling circuit these drugs modulate. This makes sodium intake a particularly relevant environmental modifier for STK39 variant carriers.

The evidence for blood pressure effects of sodium restriction is well-established, but the magnitude of response varies substantially by genetic background — individuals with variants in salt-handling genes (WNK1, WNK4, NCC, SPAK) tend to show stronger blood pressure responses to sodium changes than those without. This genotype provides a rationale for stricter sodium monitoring and early blood pressure tracking.

Interactions

rs35929607 exists on the same haplotype as rs6749447 and rs3754777, two other STK39 intronic variants studied in the same populations. These three variants show strong epistatic interaction: the combined three-SNP model predicts hypertension substantially better than any variant alone. See rs3754777 for the STK39 variant with stronger independent evidence (OR=5.9 in the BELHYPGEN cohort for the TT genotype). Any compound action should consider all three loci together.

The WNK-SPAK-NCC axis interacts with potassium balance: hypokalemia activates WNK bodies that cluster WNK4 and SPAK to amplify NCC activity, increasing sodium retention and blood pressure. Carriers of STK39 variants who also have low dietary potassium may show compounded effects on sodium handling.

Genotype Interpretations

What each possible genotype means for this variant.

AA Normal

No elevated blood pressure risk from this STK39 variant

You carry two copies of the A allele at rs35929607, the most common genotype globally. About 53% of people share this genotype. The WNK-SPAK-NCC kidney sodium-handling pathway operates at its typical baseline without the additional influence of the G allele at this locus. Your blood pressure regulation from this variant is unremarkable.

AG Intermediate

Mild potential increase in salt sensitivity through SPAK pathway

You carry one copy of the G allele at rs35929607. About 40% of people share this genotype. The G allele has been nominally associated with modestly higher blood pressure in some populations — particularly a Pakistani cohort reporting approximately 3 mmHg higher systolic blood pressure per G allele — but this association was not replicated in a pooled meta-analysis. The evidence is most consistent with a modest increase in salt sensitivity mediated through the WNK-SPAK-NCC sodium reabsorption axis, rather than a large independent hypertension risk effect.

GG High Risk

Homozygous for the STK39 variant allele — possible heightened salt sensitivity

The WNK-SPAK-NCC axis is the primary molecular target of thiazide diuretics, the most prescribed antihypertensive class globally. When SPAK is more active or more abundant, NCC phosphorylation is increased, sodium reabsorption from the distal tubule rises, plasma volume expands, and blood pressure climbs. Variants in this pathway that increase SPAK expression (as suggested by the cis-eQTL data at this locus) therefore produce a phenotype qualitatively similar to what thiazide diuretics suppress. For GG carriers, the most actionable interpretation is to treat the kidney's sodium circuit as more "active" than average — which makes sodium intake control and blood pressure monitoring especially relevant. A Pakistani cohort found that GG homozygotes who also had age >50, diabetes, or BMI >23 had 12-fold higher hypertension rates, suggesting additive environmental loading on the genetic substrate.