What you carry at this position in your DNA and what research says about it.
Cardiovascular Risk: 9/10 evidence, 12 publications.
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Sample genotype (not yours): G/G
Typical Cardiovascular Risk and Normal PLTP Activity
Standard PLTP activity levels maintain typical lipid remodeling and average cardiovascular risk.
What this genotype means: Typical PLTP activity; Larger HDL particle size; Standard cardiovascular risk.
Sample genotype (not yours): A/A
Lowest Cardiovascular Risk and Significantly Reduced PLTP Activity
Carrying two copies of the protective A allele maximizes the reduction in PLTP activity, offering the strongest protection against carotid artery disease. This genotype promotes highly efficient cholesterol clearance.
What this genotype means: Significantly reduced PLTP activity; Smaller HDL particle size; Lowest cardiovascular risk.
Sample genotype (not yours): G/A
Lower Cardiovascular Risk and Reduced PLTP Activity
Carrying one copy of the protective A allele reduces PLTP activity and lowers the risk of carotid artery disease. This change shifts HDL particles to smaller, highly active forms.
What this genotype means: Reduced PLTP activity; Smaller HDL particle size; Lower cardiovascular risk.
Gene function and biological role
Gene Function: Phospholipid transfer protein, encoded by the PLTP gene, plays a critical role in remodeling high-density lipoprotein particles in the bloodstream [1]. It facilitates the transfer of phospholipids and free cholesterol from triglyceride-rich lipoproteins to HDL [1]. This process is essential for the maturation of HDL and the generation of smaller, lipid-poor particles that participate in reverse cholesterol transport [1]. Elevated PLTP activity has been linked to pro-atherogenic processes and an increased risk of cardiovascular disease in human cohorts [2]. Conversely, genetically lower PLTP expression is associated with a more favorable cardiovascular profile [2].
Variant Impact: The rs6065904 variant is an intronic change in the PLTP gene that influences how efficiently the protein is transcribed and active in the blood [1]. The minor A allele is strongly associated with reduced PLTP transcription in the liver and lower overall plasma PLTP activity [1]. This reduction in activity alters the size distribution of HDL particles, shifting them toward smaller, more numerous subfractions [3]. Although smaller HDL particles are sometimes viewed as less traditional, genetic studies show they are highly protective against carotid artery disease and general cardiovascular events [1].
Key Insight: Lower PLTP activity actually protects against heart disease, even though it results in smaller HDL particles and slightly higher LDL cholesterol.
Location: PLTP. Chromosome 20 · 20q13.12 · 45.9 Mb
Estimated prevalence by population
Global 58.4%; European 61.1%; African 60.3%; East Asian 45.1%; South Asian 45.2%; Americas 47.5%; Ashkenazi 63.5%; Finnish 58.9%; Middle Eastern 67.7%; Amish 65.2%.
Estimated GG genotype frequency.
Global 35.9%; European 34.1%; African 34.7%; East Asian 44.1%; South Asian 44.0%; Americas 42.8%; Ashkenazi 32.4%; Finnish 35.7%; Middle Eastern 29.1%; Amish 31.1%.
Estimated GA genotype frequency.
Global 5.7%; European 4.8%; African 5.0%; East Asian 10.8%; South Asian 10.7%; Americas 9.6%; Ashkenazi 4.1%; Finnish 5.4%; Middle Eastern 3.1%; Amish 3.7%.
Estimated AA genotype frequency.
Showing effects for G/G genotype
Cardiovascular & Metabolic
Heart Disease
Cardiovascular Risk. Evidence: 4/10. Source: PMID 19965587. Typical Risk.
Lipids & Cholesterol
PLTP Activity. Evidence: 3/10. Source: PMID 19965587. Typical.
HDL Particle Size. Evidence: 8/10. Source: PMID 35213538. Larger Particles.
LDL Cholesterol. Evidence: 9/10. Source: PMID 32154731. Typical.
Free Cholesterol in HDL. Evidence: 9/10. Source: PMID 41044249. Higher.
Showing effects for A/A genotype
Cardiovascular Risk. Evidence: 4/10. Source: PMID 19965587. Lowest Risk.
PLTP Activity. Evidence: 3/10. Source: PMID 19965587. Significantly Reduced.
HDL Particle Size. Evidence: 8/10. Source: PMID 35213538. Smaller Particles.
LDL Cholesterol. Evidence: 9/10. Source: PMID 32154731. Slightly Higher.
Free Cholesterol in HDL. Evidence: 9/10. Source: PMID 41044249. Lower.
Showing effects for G/A genotype
Cardiovascular Risk. Evidence: 4/10. Source: PMID 19965587. Reduced Risk.
PLTP Activity. Evidence: 3/10. Source: PMID 19965587. Reduced.
What this genotype means for the people who carry it
Sample genotype: GG (Homozygous)
Standard PLTP activity is maintained by this genotype, resulting in typical phospholipid transfer rates during lipoprotein remodeling [1]. This activity level supports the formation of larger HDL particles, which are traditionally measured as higher HDL cholesterol on standard blood tests [1]. However, larger HDL size does not necessarily translate to better cardiovascular protection, as higher PLTP activity is associated with increased carotid artery disease risk [1]. This genotype is linked to typical baseline risk for cardiovascular events and carotid artery thickening [1]. Standard LDL cholesterol levels are also typically lower compared to those with the minor allele [2].
Typical PLTP activity; Larger HDL particle size; Standard cardiovascular risk.
Sample genotype: AA (Homozygous)
Carrying two copies of the minor A allele results in the lowest levels of PLTP transcription and plasma activity [1]. This significant reduction in protein activity shifts the lipid profile toward smaller, more numerous HDL particles [2]. These smaller particles are exceptionally active in reverse cholesterol transport, facilitating rapid clearance of arterial lipids [1]. As a result, this genotype provides the strongest genetic protection against carotid artery disease and cardiovascular events [1]. Although standard LDL cholesterol and glycoprotein acetyls may be slightly elevated, the overall cardiovascular risk is significantly reduced [2]. This unique lipid profile demonstrates that HDL particle quality and size are often more important than total HDL cholesterol numbers.
Significantly reduced PLTP activity; Smaller HDL particle size; Lowest cardiovascular risk.
Sample genotype: GA (Heterozygous)
Carrying one copy of the minor A allele is associated with a significant reduction in plasma PLTP activity and hepatic transcription [1]. This reduction alters lipoprotein remodeling, leading to a higher concentration of smaller, highly functional HDL particles [2]. These smaller HDL subfractions are highly efficient at clearing cholesterol from blood vessels, which reduces the risk of plaque buildup [1]. Consequently, this genotype is linked to a lower risk of carotid artery disease and general cardiovascular events [1]. While standard LDL cholesterol levels may be slightly higher, the overall net effect on cardiovascular health remains protective [2].
Reduced PLTP activity; Smaller HDL particle size; Lower cardiovascular risk.
Variants with shared genetic architecture
rs4810479 · PLTP Gene · Chr 20 · HDL and Triglycerides
rs6065906 · PLTP Gene · Chr 20 · Cardiovascular Health
rs6073958 · PLTP Gene · Chr 20 · Blood Lipid Levels
Genetic and nongenetic sources of variation in phospholipid transfer protein activity.
Polygenic Hyperlipidemias and Coronary Artery Disease Risk.
Content updated August 2026.
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