What you carry at this position in your DNA and what research says about it.
HDL Cholesterol Levels: 10/10 evidence, 16 publications.
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Sample genotype (not yours): A/A
Typical HDL Cholesterol and Lipid Levels
Standard LCAT enzyme activity supports typical levels of HDL cholesterol and other circulating lipids.
What this genotype means: Typical LCAT enzyme activity; Standard baseline HDL cholesterol levels.
Sample genotype (not yours): A/T
Slightly Lower HDL Cholesterol Levels
A mild reduction in LCAT enzyme activity leads to slightly lower HDL cholesterol levels without increasing heart disease risk.
What this genotype means: Mildly reduced LCAT enzyme activity; Slightly lower circulating HDL cholesterol.
Sample genotype (not yours): T/T
Significantly Lower HDL Cholesterol Levels
Reduced LCAT enzyme activity significantly lowers HDL cholesterol levels, but does not raise the risk of heart disease.
What this genotype means: Reduced LCAT enzyme activity; Significantly lower circulating HDL cholesterol.
Gene function and biological role
Gene Function: The LCAT gene encodes lecithin-cholesterol acyltransferase, an enzyme crucial for lipid metabolism [1]. This enzyme converts free cholesterol into cholesteryl esters, which are then packaged into high-density lipoprotein (HDL) particles [1]. This process is a key step in reverse cholesterol transport, which helps clear excess cholesterol from peripheral tissues and return it to the liver [1]. While severe mutations in LCAT can cause rare genetic disorders, common variations often lead to milder differences in circulating lipid levels [2].
Variant Impact: A single-nucleotide change in the LCAT gene alters the encoded amino acid from serine to threonine at position 232 [1]. This structural change alters the enzyme's activity, leading to a reduction in the rate of cholesterol esterification [1]. Consequently, individuals carrying the variant allele tend to have lower levels of circulating HDL cholesterol [1]. Despite this reduction in HDL, clinical databases classify this variant as benign, meaning it does not cause severe LCAT deficiency disorders [2].
Key Insight: Although this variant significantly lowers HDL (good) cholesterol, large-scale genetic studies show it does not increase the risk of heart attacks, challenging the traditional view that HDL levels directly cause heart disease.
Location: LCAT. Chromosome 16 · 16q22.1 · 67.9 Mb
Estimated prevalence by population
Global 96.6%; European 94.3%; African 99.0%; East Asian 100.0%; South Asian 98.7%; Americas 98.4%; Ashkenazi 99.9%; Finnish 94.7%; Middle Eastern 100.0%; Amish 96.9%.
Estimated AA genotype frequency.
Global 3.4%; European 5.6%; African 1.0%; East Asian 0.0%; South Asian 1.3%; Americas 1.6%; Ashkenazi 0.1%; Finnish 5.3%; Middle Eastern 0.0%; Amish 3.0%.
Estimated AT genotype frequency.
Global < 0.1%; European 0.1%; African < 0.1%; East Asian 0.0%; South Asian < 0.1%; Americas < 0.1%; Ashkenazi < 0.1%; Finnish 0.1%; Middle Eastern 0.0%; Amish < 0.1%.
Estimated TT genotype frequency.
Showing effects for A/A genotype
Cardiovascular & Metabolic
Lipids & Cholesterol
HDL Cholesterol. Evidence: 10/10. Source: PMID 22090275. Typical Levels.
Total Cholesterol. Evidence: 10/10. Source: PMID 33462484. Typical Levels.
Apolipoprotein A1. Evidence: 10/10. Source: PMID 33462484. Typical Levels.
Nutrition & Metabolism
Macronutrient Metabolism
Omega-3 Fatty Acids. Evidence: 10/10. Source: PMID 40545721. Typical Levels.
Showing effects for A/T genotype
HDL Cholesterol. Evidence: 10/10. Source: PMID 22090275. Lower Levels.
Total Cholesterol. Evidence: 10/10. Source: PMID 33462484. Slightly Lower.
Apolipoprotein A1. Evidence: 10/10. Source: PMID 33462484. Slightly Lower.
Omega-3 Fatty Acids. Evidence: 10/10. Source: PMID 40545721. Slightly Higher.
Showing effects for T/T genotype
HDL Cholesterol. Evidence: 10/10. Source: PMID 22090275. Significantly Lower.
Total Cholesterol. Evidence: 10/10. Source: PMID 33462484. Lower Levels.
Apolipoprotein A1. Evidence: 10/10. Source: PMID 33462484. Lower Levels.
Omega-3 Fatty Acids. Evidence: 10/10. Source: PMID 40545721. Higher Levels.
What this genotype means for the people who carry it
Sample genotype: AA (Homozygous)
Most people worldwide carry two copies of the common A allele, which maintains standard LCAT enzyme function. Having two copies of the A allele means your LCAT enzyme functions at a standard baseline level [1]. This enzyme is responsible for esterifying cholesterol, a critical step in forming mature HDL particles [1]. Consequently, you are likely to have typical levels of HDL cholesterol, total cholesterol, and apolipoprotein A1 [2]. While observational studies historically linked higher HDL to better heart health, genetic studies using this variant show that HDL levels alone do not causally dictate heart attack risk [1]. Your cardiovascular risk is therefore shaped by standard lifestyle and genetic factors rather than this specific variant.
Typical LCAT enzyme activity; Standard baseline HDL cholesterol levels.
Sample genotype: AT (Heterozygous)
Approximately three percent of people of European ancestry carry one copy of the T allele. Carrying one copy of the T allele slightly reduces the efficiency of the LCAT enzyme in esterifying cholesterol [1]. As a result, individuals with this genotype typically experience a modest reduction of about 13% in their circulating HDL cholesterol levels [1]. Interestingly, although lower HDL is traditionally viewed as a risk factor, large-scale Mendelian randomization studies show that this genetically driven reduction does not increase the risk of myocardial infarction [1]. This finding has been pivotal in showing that HDL cholesterol levels may not be causally linked to heart disease [1]. Clinical databases confirm this variant is entirely benign and does not cause severe metabolic disorders [2].
Mildly reduced LCAT enzyme activity; Slightly lower circulating HDL cholesterol.
Sample genotype: TT (Homozygous)
Less than one in a thousand people globally carry two copies of the T allele. Having two copies of the T allele reduces the activity of the LCAT enzyme, which is responsible for converting free cholesterol into cholesteryl esters [1]. This reduction leads to a pronounced decrease in circulating HDL cholesterol and apolipoprotein A1 levels [1]. However, clinical evaluations have confirmed that this variant is benign and does not cause severe LCAT deficiency syndromes like Norum disease or Fish-eye disease [2]. Furthermore, genetic studies demonstrate that the lower HDL levels associated with this genotype do not translate to an increased risk of heart attacks [1]. This supports the medical consensus that genetically low HDL cholesterol is not a direct cause of cardiovascular disease.
Reduced LCAT enzyme activity; Significantly lower circulating HDL cholesterol.
Variants with shared genetic architecture
rs10096633 · LPL Gene · Chr 8 · Triglycerides and Heart Health
rs10468017 · LIPC Gene · Chr 15 · Cholesterol and Eye Health
rs12720922 · CETP Gene · Chr 16 · Cholesterol and Heart Health
LipidSeq: a next-generation clinical resequencing panel for monogenic dyslipidemias.
Genetics of 35 blood and urine biomarkers in the UK Biobank.
Content updated August 2026.
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