rs4240624 — PPP1R3B Near-gene variant

Intronic PPP1R3B variant that increases hepatic glycogen accumulation, elevating liver enzymes and raising the risk of non-alcoholic fatty liver disease and gallstones

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PPP1R3B — The Hidden Glycogen Switch in Your Liver

Most people have never heard of glycogen as a liver health problem. Fat — specifically NAFLD11 NAFLD
Non-alcoholic fatty liver disease: excess fat accumulation in liver cells unrelated to alcohol consumption, affecting roughly 25% of the global population — gets all the attention. But for carriers of the rs4240624 G allele, the issue begins one step earlier in liver metabolism: the regulation of glycogen22 glycogen
The body's main short-term glucose storage molecule. The liver stores glycogen and releases glucose into the blood between meals to maintain stable blood sugar levels synthesis.

PPP1R3B encodes a regulatory subunit of protein phosphatase 1 (PP1), a master switch that controls glycogen metabolism in the liver. The G allele at rs4240624 — carried by roughly 10% of Europeans and 19% of people of African descent — influences how much glycogen the liver stores, pushing the balance toward accumulation. The downstream effects extend beyond glycogen: elevated liver enzymes, increased NAFLD susceptibility, and a meaningful increase in gallstone risk have all been documented across large population studies.

The Mechanism

Protein phosphatase 133 Protein phosphatase 1
PP1: one of the most abundant phosphatases in the body, involved in glycogen metabolism, muscle contraction, protein synthesis, and many other processes. Its activity is tightly regulated by dozens of binding proteins (PP1) is a central regulator of glycogen metabolism. PPP1R3B acts as a glycogen-targeting subunit that directs PP1 to two key enzymes: glycogen synthase (which builds glycogen) and glycogen phosphorylase (which breaks it down). By activating glycogen synthase and inhibiting glycogen phosphorylase, PPP1R3B tips the liver toward glycogen storage.

The rs4240624 G allele is a near-gene regulatory variant that increases PPP1R3B activity or expression. Mouse studies confirm the mechanism directly: overexpression of PPP1R3B causes hepatic glycogen accumulation and elevated plasma ALT, while knockouts produce glycogen-deficient livers. In humans, the minor G allele is associated with increased hepatic X-ray attenuation — a hallmark of glycogen loading — and elevated liver enzymes across multiple large cohorts (n=112,428 in the definitive Stender 2018 study).

Importantly, the excess glycogen from this variant does not appear to directly increase hepatic triglyceride content. This distinguishes rs4240624 from the well-known PNPLA3 rs738409 variant, which directly promotes liver fat accumulation. Instead, the PPP1R3B effect reflects hepatic glycogenosis44 hepatic glycogenosis
Abnormal glycogen accumulation in the liver. Can cause hepatomegaly and elevated liver enzymes, and is associated with metabolic syndrome even in the absence of excess fat, a condition that is independently harmful even without steatosis.

The bile and gallstone connection is mechanistically distinct: altered hepatic glycogen-lipid flux changes the composition of bile produced by the liver, with G-allele carriers showing higher concentrations of lithogenic (stone-forming) bile lipid classes. A 2024 validation in the UK Biobank confirmed elevated gallstone disease rates in G carriers with obesity.

The Evidence

The foundational work comes from Stender et al. 201855 Stender et al. 2018
Stender S, Smagris E, et al. "Relationship between genetic variation at PPP1R3B and levels of liver glycogen and triglyceride." Hepatology, 2018, which analyzed 112,428 participants across three large cohorts. The minor allele showed consistent ALT elevation (P = 3×10⁻⁴ in the Copenhagen cohort; P = 0.004 in the Dallas Heart Study), and liver disease odds ratios of 1.13–1.23. Crucially, no association was found with hepatic triglyceride content, pointing specifically at glycogen as the culprit.

Hernaez et al. 201366 Hernaez et al. 2013
Hernaez R, McLean J, et al. "Association between variants in or near PNPLA3, GCKR, and PPP1R3B with ultrasound-defined steatosis." Clin Gastroenterol Hepatol, 2013 used NHANES III data (n=4,804) and found an OR of 1.28 (P=.03) for ultrasound-defined hepatic steatosis in non-Hispanic white adults — suggesting that glycogen accumulation in the liver may mimic the appearance of steatosis on standard ultrasound, even when triglycerides are not elevated.

The gallstone connection was established by Männistö et al. 2021 and 202477 Männistö et al. 2021 and 2024
Männistö VT, Kaminska D, et al. Hepatol Commun 2021; Gastro Hep Adv 2024, who found that among bariatric surgery patients, the G allele produced dramatically different bile acid profiles (total bile acids 35 vs. 109 mM in G carriers vs. non-carriers) and that 13 of 17 bile lipid classes were elevated in G carriers — a pattern that mirrors bile composition in gallstone patients.

A 2024 Taiwan Biobank study (n=150,709) confirmed rs4240624 among seven SNPs significantly associated with metabolic syndrome, underscoring its relevance across diverse populations with high metabolic disease burden.

Practical Actions

For G allele carriers, the primary risk is a liver that stores too much glycogen, especially in the context of a high-carbohydrate diet and metabolic syndrome. Actionable steps center on reducing hepatic glycogen load, supporting liver health, and monitoring for early signs of liver stress and gallstones.

Dietary strategies should focus on moderating refined carbohydrate intake — the primary driver of hepatic glycogen synthesis. Time-restricted eating and reduced meal frequency allow glycogen to be depleted between meals. Avoiding prolonged high-carbohydrate loads (particularly fructose, which is processed almost entirely by the liver) reduces the burden on hepatic glycogen pathways.

Regular liver enzyme monitoring (ALT/AST) is the most direct way to track whether hepatic glycogenosis is causing organ stress. Elevated ALT in the absence of significant hepatic fat on ultrasound should prompt consideration of this genetic mechanism.

Given the documented gallstone risk, G carriers who are female, have obesity, or have additional risk factors should discuss gallstone screening with their physician, especially before planned rapid weight loss (which can mobilize bile cholesterol and precipitate stone formation).

Interactions

PPP1R3B rs4240624 does not appear to directly interact with other common liver SNPs at the molecular level, but its effects are expected to be additive with PNPLA3 rs738409 (the most common NAFLD gene variant) and GCKR rs780094 (a glucokinase regulator also associated with hepatic fat and triglycerides). Individuals carrying risk alleles at multiple these loci face compounding liver stress through distinct pathways — glycogen overload (PPP1R3B), lipid dysregulation (PNPLA3), and impaired glucose sensing (GCKR).

Nutrient Interactions

carbohydrates altered_metabolism
fructose increased_need

Genotype Interpretations

What each possible genotype means for this variant.

AA Standard Glycogen Regulation Normal

Your liver glycogen metabolism follows the common pattern

You carry two copies of the common A allele at PPP1R3B rs4240624. Your hepatic glycogen regulation is not influenced by this variant, and you do not have the elevated liver enzyme or glycogen accumulation risk associated with the G allele. This genotype is found in roughly 76% of people of European descent.

AG One Copy — Moderate Risk Intermediate

One G allele — modestly elevated risk of hepatic glycogen accumulation

The G allele increases the activity of PPP1R3B, a key regulatory subunit that targets protein phosphatase 1 (PP1) to promote hepatic glycogen synthesis. With one G copy, this effect is intermediate: the liver stores somewhat more glycogen than typical, which can manifest as mildly elevated ALT/AST on blood tests even without significant hepatic fat on imaging. The Stender 2018 study (n=112,428) documented consistent ALT elevation across multiple cohorts in heterozygous carriers.

The gallstone risk is also relevant for AG carriers, particularly in the context of obesity. Research in bariatric surgery patients demonstrated altered bile lipid profiles beginning in heterozygous individuals, with the bile composition tilting toward lithogenic (stone-forming) patterns.

GG Two Copies — Higher Risk High Risk

Two G alleles — elevated hepatic glycogen accumulation risk and gallstone susceptibility

Homozygous G carriers at rs4240624 have two copies of the variant that increases PPP1R3B expression and activity. This means hepatic PP1 is more strongly directed toward glycogen synthesis on both alleles simultaneously, leading to the greatest degree of glycogen accumulation in the liver among carriers. Mouse models of PPP1R3B overexpression directly replicate this phenotype, showing hepatic glycogen accumulation along with elevated plasma ALT — mirroring the human genetic findings.

The 2021 Männistö study found dramatic differences in bile composition for individuals carrying the G allele, including total bile acid concentrations of 35 mM vs. 109 mM in non-carriers. This highly altered bile lipidome is associated with a substantial increase in gallstone risk, particularly in individuals with obesity. The 2024 validation in the UK Biobank confirmed elevated gallstone disease rates in G carriers.

GG carriers should be proactive about liver monitoring, carbohydrate management, and gallstone risk assessment — especially if they have metabolic syndrome, obesity, or are planning rapid weight loss.