rs3829462 — LIPC

Missense variant in hepatic lipase encoding p.Phe356Leu; the rare C allele (Phe356) is the GRCh38 reference but represents the minority allele globally, while the common A allele (Leu356) is found in ~97% of people and classified benign

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LIPC — Hepatic Lipase and HDL Particle Remodeling

Hepatic lipase (HL), encoded by the LIPC gene on chromosome 15, is a key enzyme in lipoprotein metabolism. It sits on liver sinusoid endothelium and acts as a lipase and ligand for lipoprotein uptake — hydrolyzing triglycerides and phospholipids in HDL and intermediate-density lipoproteins (IDL). Its best-known role is converting large, buoyant HDL2 particles into smaller, denser HDL3, a step that completes the reverse cholesterol transport11 reverse cholesterol transport
the process by which excess cholesterol from peripheral tissues is ferried back to the liver for elimination or bile excretion cycle.

The rs3829462 variant causes a missense substitution at codon 356: phenylalanine (Phe, encoded by the C reference allele) to leucine (Leu, encoded by the common A allele). This is an unusual configuration — the GRCh38 reference carries the minor allele (C, ~2.6% globally), while the overwhelmingly common A allele (Leu356, ~97.4%) represents the normal population baseline.

The Mechanism

Phenylalanine and leucine are both nonpolar hydrophobic amino acids, which explains why computational tools (SIFT score 0.26, PolyPhen 0.137) classify this substitution as tolerated and benign. Position 356 lies in the C-terminal domain of hepatic lipase, a region involved in lipoprotein binding and heparin-sulfate proteoglycan interaction. The Phe→Leu change at this position preserves the hydrophobic character of the side chain, and no published functional studies have demonstrated that the C allele (Phe356) substantially alters enzyme catalysis, substrate affinity, or secretion.

Nonetheless, the variant falls within the LIPC gene, which encodes an enzyme whose activity is a primary determinant of HDL particle size distribution and triglyceride clearance from HDL. Full hepatic lipase deficiency (OMIM 15167022 OMIM 151670
autosomal recessive condition causing elevated HDL-C and hypertriglyceridemia due to impaired IDL and HDL remodeling) produces markedly elevated HDL-C with paradoxically elevated triglycerides and pro-atherogenic dyslipidemia. Heterozygous loss-of-function LIPC variants produce milder lipid phenotypes, including modestly elevated total cholesterol, LDL-C, and triglycerides, as Jacob et al.33 Jacob et al.
Jacob EO et al. Phenotype in Individuals with Heterozygous Rare Variants in LIPC Encoding Hepatic Lipase. Atherosclerosis, 2024 showed in 46 heterozygous rare-variant carriers.

The Evidence

ClinVar classifies the A (Leu356) allele as Benign across three independent submissions (VCV000316673), citing allele frequency analysis showing the variant is far too common (~97.4%) to cause a rare Mendelian disease. The allele was identified in large population sequencing studies (Stahnke et al.44 Stahnke et al.
Stahnke G et al. Human hepatic triglyceride lipase: cloning of the gene and expression/secretion of the recombinant enzyme. J Biol Chem, 1987) and documented as a natural variant in UniProt (P11150).

The broader LIPC literature establishes that reduced hepatic lipase activity has complex cardiovascular consequences. A study of normolipidemic Brazilian participants55 study of normolipidemic Brazilian participants
Zago VHS et al. Lipase C, Hepatic Type -250A/G (rs2070895) Variant Enhances Carotid Atherosclerosis. Mol Genet Metab, 2020 found that a promoter variant reducing HL activity by 38% raised carotid plaque risk 3.9-fold despite higher HDL-C — because impaired HL produces dysfunctional HDL particles enriched in triglycerides and depleted in cholesteryl esters, less capable of effective reverse cholesterol transport.

For rs3829462 specifically, the evidence remains at the emerging level: the variant is catalogued, computationally predicted benign, and clinically classified as benign/uncertain. No dedicated functional or epidemiological studies have directly characterized the Phe356Leu substitution's effect on hepatic lipase activity or lipid phenotype.

Practical Actions

For the rare CC genotype (homozygous Phe356), the uncertainty warrants monitoring lipid subfractions — particularly HDL particle size distribution, triglycerides, and LDL particle count — to detect any functional HL impairment reflected in lipoprotein composition. Omega-3 fatty acids (EPA/DHA) can modulate hepatic lipase activity and triglyceride-rich lipoprotein clearance independently of genotype, making supplementation a reasonable adjunct.

For the AC heterozygote (~5% of people), the single C allele is unlikely to produce clinically meaningful HL impairment given the benign computational predictions and the high frequency of the A allele in the heterozygous state. Standard lipid monitoring remains appropriate.

Interactions

The biological effects of LIPC variants interact with CETP (rs708272, rs1800775), whose product transfers cholesteryl esters from HDL to LDL. The combination of reduced HL activity and altered CETP function can additively shift lipoprotein particle distributions. Isaacs et al.66 Isaacs et al.
Isaacs A et al. Epistatic effect of CETP and LIPC on serum HDL-C. Arterioscler Thromb Vasc Biol, 2007 showed epistatic interaction between LIPC and CETP variants on HDL-C, with individuals homozygous for both variants showing the largest HDL elevations — yet without reduced atherosclerosis risk, highlighting that HL-driven HDL particle quality matters more than quantity.

LIPC promoter variants (rs1800588 C-514T, rs2070895 -250G/A) also affect HL expression and interact with adiposity and visceral fat distribution to modulate HDL subclass composition, particularly the HDL2/HDL3 ratio.

Nutrient Interactions

omega-3 fatty acids altered_metabolism

Genotype Interpretations

What each possible genotype means for this variant.

AA Normal

Common Leu356 genotype — normal hepatic lipase activity

You carry two copies of the A allele (Leu356), the overwhelmingly common form of hepatic lipase found in approximately 95% of people globally. This genotype is classified Benign by ClinVar and is predicted to preserve normal hepatic lipase function. Your LIPC gene is expected to produce hepatic lipase with standard activity for HDL remodeling and triglyceride hydrolysis.

AC Intermediate

One copy of the rare Phe356 allele — likely no meaningful effect

You carry one copy of the C allele (Phe356), present in approximately 5% of people. The heterozygous AC genotype carries one copy of the rarer hepatic lipase variant alongside the common Leu356 allele. Computational tools (SIFT, PolyPhen) predict the Phe→Leu substitution is tolerated and benign, and ClinVar classifies this variant as Benign based on its high population frequency. Heterozygous carriers of rare LIPC variants can show modest lipid differences, but for this specific variant, functional impairment is unlikely.

CC High Risk

Rare Phe356 homozygous genotype — uncertain hepatic lipase function, monitor lipoprotein subfractions

The rs3829462 CC genotype has not been studied in isolation in functional assays or clinical cohorts. The inference that it may affect hepatic lipase function comes from the gene's biological role and the pattern seen with other LIPC rare variants. Jacob et al. (2024, PMID 39518997) showed that heterozygous carriers of rare LIPC pathogenic variants have significantly elevated total cholesterol, LDL-C, and triglycerides — a semi-dominant rather than purely recessive inheritance pattern for LIPC loss-of-function.

However, rs3829462 is not classified as pathogenic or likely pathogenic; its "uncertain" designation here reflects that functional evidence is absent rather than that harm has been demonstrated. A fasting lipid assessment including HDL particle size or NMR lipoprotein subfraction analysis would determine whether this genotype has any measurable effect on lipoprotein composition in your specific case.