rs2000813 — LIPG

Missense variant in endothelial lipase that tags a regulatory haplotype associated with modestly higher HDL cholesterol through reduced LIPG expression

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LIPG — The Endothelial Lipase That Shapes Your HDL

Your HDL cholesterol is not just a passive bystander in cardiovascular health — it is actively dismantled and rebuilt by a family of enzymes, and endothelial lipase (EL)11 endothelial lipase (EL)
Encoded by the LIPG gene on chromosome 18; the only lipase secreted specifically from vascular endothelial cells is one of the primary drivers of HDL catabolism. Unlike lipoprotein lipase (which targets triglyceride-rich particles), EL preferentially hydrolyzes the phospholipid surface of HDL, accelerating its breakdown and removal from circulation. Higher EL activity means lower HDL; lower EL activity means higher HDL. The rs2000813 variant is a common missense change in LIPG that, through an indirect regulatory mechanism, is associated with modestly higher HDL cholesterol in carriers of the T allele.

The Mechanism

The rs2000813 variant produces a Thr111Ile substitution22 Thr111Ile substitution
A change from threonine to isoleucine at amino acid position 111 of the endothelial lipase protein in the LIPG protein. Careful in vitro studies have shown that the Ile111 variant has essentially identical phospholipase activity, protein stability, and regulation by ANGPTL3 and ANGPTL433 ANGPTL3 and ANGPTL4
Angiopoietin-like proteins 3 and 4 are endogenous inhibitors of endothelial lipase; they bind and inactivate EL on the surface of vascular cells compared to the wild-type enzyme. The amino acid change itself is therefore functionally silent.

The HDL association arises through a different route. The Ile111-encoding T allele is in high linkage disequilibrium44 high linkage disequilibrium
LD means the two alleles are inherited together on the same chromosomal segment so frequently that knowing one predicts the other with high accuracy (R²=0.8) with rs34474737, a variant in the 5' UTR of LIPG that directly reduces promoter activity and lowers EL expression. Carriers of the T allele at rs2000813 therefore tend to have lower circulating EL levels — not because the enzyme works differently, but because less of it is produced. Lower EL expression → slower HDL phospholipid hydrolysis → higher HDL-C. The coding variant is a marker for the regulatory variant, not the causal agent.

The Evidence

The GLGC (Global Lipids Genetics Consortium)55 GLGC (Global Lipids Genetics Consortium)
One of the largest GWAS consortia for lipid traits, combining data from dozens of cohorts and hundreds of thousands of participants meta-analysis found rs2000813 associated with HDL-C at genome-wide significance (β = −0.15 SD per T allele, P = 1.92×10⁻¹⁴), corresponding to approximately 2 mg/dL higher HDL-C per T allele carried. The T allele was also associated with higher HDL2, HDL3, and apoA-I.

Huang et al. (2019)66 Huang et al. (2019)
LIPG SNPs, their haplotypes and gene-environment interactions on serum lipid levels; 2,498 adults from Maonan and Han Chinese populations (Lipids in Health and Disease) replicated the HDL and apoA-I association in two East Asian ethnic groups after Bonferroni correction, adding population diversity to the dataset.

Crucially, higher HDL from this variant does not appear to translate into cardiovascular protection. Vergeer et al. (2009)77 Vergeer et al. (2009)
T111I variant in the endothelial lipase gene and risk of coronary heart disease in three independent populations; combined n=4,107 CHD cases from DCH, Nurses' Health Study, and Health Professionals Follow-up Study (European Heart Journal) found a pooled CHD odds ratio of 0.95 (95% CI 0.85–1.06) — statistically null. Mean HDL differences between T allele carriers and non-carriers were only 0–1 mg/dL within each cohort, consistent with the modest effect size seen in the GWAS. This finding aligns with the broader body of evidence showing that genetically elevated HDL does not always protect against atherosclerosis88 genetically elevated HDL does not always protect against atherosclerosis
The HDL hypothesis has faced repeated setbacks in Mendelian randomization studies, suggesting HDL quantity and HDL function are different traits.

The 2024 biochemical study99 2024 biochemical study
Johansen et al., Endothelial lipase variant T111I does not alter inhibition by angiopoietin-like proteins, Scientific Reports definitively confirmed the protein-level neutrality of T111I and reframed rs2000813 as a marker SNP for a regulatory haplotype — an important caution against inferring direct functional consequences from coding variant annotations alone.

Practical Actions

For CC homozygotes (the common genotype with highest EL expression), the actionable insight is awareness: lower baseline HDL from higher EL activity is a genetically normal pattern, not evidence of lifestyle failure. If HDL runs low on a standard lipid panel, diet quality — specifically the ratio of polyunsaturated to saturated fat and omega-3 intake — can modulate EL activity through inflammatory pathways. LIPG expression is upregulated by pro-inflammatory cytokines, so any strategy that reduces systemic inflammation may blunt EL-driven HDL catabolism.

For CT and TT carriers, the modestly elevated HDL reflects lower EL expression rather than superior reverse cholesterol transport. Standard lipid monitoring remains appropriate; the slight HDL advantage does not warrant different cholesterol management targets.

Interactions

The rs2000813 T allele is inherited as part of a broader LIPG haplotype that also includes rs3813082, rs3744843, and the causal regulatory variant rs34474737. Haplotype analysis consistently shows stronger lipid associations than any single SNP alone. A compound action combining rs2000813 (CT or TT) with rs2278236 in ANGPTL4 (a direct inhibitor of endothelial lipase) could be informative: carriers of HDL-lowering ANGPTL4 variants on top of the CC (high-EL) LIPG genotype would represent a double-hit for depressed HDL, potentially warranting targeted omega-3 monitoring and dietary fat quality review. Both variants are in the lipid-fat-metabolism pathway.

Nutrient Interactions

omega-3 fatty acids altered_metabolism

Genotype Interpretations

What each possible genotype means for this variant.

CC Standard EL Activity Normal

Normal endothelial lipase expression and typical HDL metabolism

The CC genotype is the population-common form. EL expression in CC individuals is not attenuated by the 5'UTR regulatory variant rs34474737 (which is in high LD with the T allele at rs2000813). As a result, EL-driven HDL catabolism proceeds at normal rates. The absence of the T allele does not indicate high EL activity in a pathological sense — it simply means you lack the modest expression-dampening effect of the minor haplotype. Standard lipid panel monitoring and dietary attention to fat quality remain the primary levers for optimizing your HDL.

CT Reduced EL Expression (Het) Beneficial

One copy of the HDL-raising haplotype — modestly higher HDL expected

The T allele at rs2000813 is in high LD (R²=0.8) with the rs34474737 5'UTR variant, which reduces LIPG promoter activity. Heterozygous carriers have intermediate EL expression — lower than CC, higher than TT. In the GLGC dataset, each T allele corresponds to approximately −0.15 SD in HDL-C. For a population average of ~55 mg/dL HDL, this translates to roughly 1–2 mg/dL per allele. The 2024 biochemical study by Johansen et al. confirmed the Ile111 protein is functionally indistinguishable from wild-type, so any observed HDL elevation reflects the regulatory variant in LD, not altered enzyme kinetics. Large prospective data from the EPIC-Norfolk, DCH, NHS, and HPFS studies showed no measurable CHD risk reduction from this genotype.

TT Reduced EL Expression (Hom) Beneficial

Two copies of the HDL-raising haplotype — highest expected HDL from this locus

The TT homozygous state doubles the expression-dampening effect conferred by the LD-linked 5'UTR variant rs34474737. In the GLGC meta-analysis, the β-coefficient per T allele was −0.15 SD, so TT individuals show approximately −0.30 SD shift in HDL-C — roughly 3–4 mg/dL above the population mean at typical HDL values. The Vergeer et al. (2009) meta-analysis of three large prospective cohorts found no CHD protective effect (OR 0.95, 95% CI 0.85–1.06), consistent with Mendelian randomization evidence showing genetically elevated HDL does not uniformly reduce cardiovascular risk. The protein produced by the TT genotype (Ile111) is biochemically identical to wild-type EL in phospholipase activity, thermal stability, and ANGPTL inhibition.