What you carry at this position in your DNA and what research says about it.
Cholesterol and Liver Risk: 10/10 evidence, 29 publications.
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Sample genotype (not yours): T/T
Typical Metabolic and Liver Profile
This common genotype is associated with typical circulating lipid levels and a lower baseline risk of liver fat accumulation.
What this genotype means: Typical circulating cholesterol levels; Lower risk of liver fat accumulation; Lower risk of type 2 diabetes.
Sample genotype (not yours): C/C
Lowest Cholesterol but Highest Liver Risk
Carrying two copies of the C allele significantly lowers circulating lipids but substantially increases liver disease and diabetes risks.
What this genotype means: Lowest circulating cholesterol levels; Significantly increased risk of fatty liver disease; Higher risk of liver cirrhosis and type 2 diabetes.
Sample genotype (not yours): T/C
Lower Cholesterol with Higher Liver Risk
Carrying one copy of the C allele lowers circulating cholesterol but increases the risk of liver fat accumulation and diabetes.
What this genotype means: Lower circulating LDL cholesterol; Increased risk of liver fat accumulation; Moderately higher risk of type 2 diabetes.
Gene function and biological role
Gene Function: The SUGP1 gene encodes a protein containing SURP and G-patch domains, which plays a critical role in pre-mRNA splicing [1]. It acts as a key regulator of cholesterol metabolism by modulating the alternative splicing of HMGCR, the rate-limiting enzyme in cholesterol synthesis [2]. Splicing variations in this gene alter the stability of metabolic transcripts, directly impacting how the liver processes and secretes lipids [2]. Because of its central role in RNA splicing, SUGP1 influences both circulating blood lipid levels and fat accumulation within liver cells [1].
Variant Impact: The rs10401969 variant is located within the eighth intron of the SUGP1 gene and acts as a major metabolic modifier. The C allele of this variant alters splicing efficiency, leading to increased exon skipping and subsequent nonsense-mediated decay of the SUGP1 transcript [2]. This reduction in functional splicing activity decreases hepatic cholesterol synthesis and increases LDL receptor uptake, lowering circulating blood lipids [2]. However, this same splicing shift is in strong linkage disequilibrium with variants that impair the secretion of lipids from the liver, leading to fat accumulation in hepatic tissue [1].
Key Insight: This variant represents a direct biological trade-off where alleles that lower circulating cardiovascular risk factors simultaneously increase the risk of fat accumulation in the liver.
Location: SUGP1. Chromosome 19 · 19p13.11 · 19.3 Mb
Estimated prevalence by population
Global 81.1%; European 85.8%; African 68.8%; East Asian 81.2%; South Asian 80.6%; Americas 86.2%; Ashkenazi 90.7%; Finnish 88.8%; Middle Eastern 86.2%; Amish 78.5%.
Estimated TT genotype frequency.
Global 17.7%; European 13.7%; African 28.3%; East Asian 17.9%; South Asian 18.4%; Americas 13.3%; Ashkenazi 9.0%; Finnish 10.9%; Middle Eastern 13.3%; Amish 20.2%.
Estimated TC genotype frequency.
Global 1.2%; European 0.5%; African 2.9%; East Asian 1.0%; South Asian 1.0%; Americas 0.5%; Ashkenazi 0.2%; Finnish 0.3%; Middle Eastern 0.5%; Amish 1.3%.
Estimated CC genotype frequency.
Showing effects for T/T genotype
Organ Systems
Liver Function & Disease
Liver Cirrhosis. Evidence: 6/10. Source: PMID 32853455. Lower Risk.
Cardiovascular & Metabolic
Lipids & Cholesterol
LDL Cholesterol. Evidence: 10/10. Source: PMID 20686565. Higher Levels.
Triglycerides. Evidence: 10/10. Source: PMID 20686565. Higher Levels.
Diabetes & Glycemic Traits
Type 2 Diabetes. Evidence: 7/10. Source: PMID 22885922. Lower Risk.
Showing effects for C/C genotype
Liver Cirrhosis. Evidence: 6/10. Source: PMID 32853455. ~1.7x Higher Risk.
LDL Cholesterol. Evidence: 10/10. Source: PMID 20686565. Lowest Levels.
Triglycerides. Evidence: 10/10. Source: PMID 20686565. Lowest Levels.
Type 2 Diabetes. Evidence: 7/10. Source: PMID 22885922. ~1.13x Higher Risk.
Showing effects for T/C genotype
Liver Cirrhosis. Evidence: 6/10. Source: PMID 32853455. Increased Risk.
LDL Cholesterol. Evidence: 10/10. Source: PMID 20686565. Lower Levels.
Triglycerides. Evidence: 10/10. Source: PMID 20686565. Lower Levels.
Type 2 Diabetes. Evidence: 7/10. Source: PMID 22885922. Increased Risk.
What this genotype means for the people who carry it
Sample genotype: TT (Homozygous)
Most individuals carry two copies of the T allele, representing the baseline metabolic profile in the general population. This genotype is associated with slightly higher circulating levels of LDL cholesterol and triglycerides compared to carriers of the C allele [1]. However, because lipids are efficiently exported from the liver into the bloodstream, this profile is protective against hepatic fat buildup [2]. Consequently, there is a lower baseline risk for non-alcoholic fatty liver disease and liver cirrhosis [3]. The risk for type 2 diabetes is also lower compared to C allele carriers [4].
Typical circulating cholesterol levels; Lower risk of liver fat accumulation; Lower risk of type 2 diabetes.
Sample genotype: CC (Homozygous)
This rare genotype maximizes the metabolic trade-off associated with the SUGP1 locus. Carrying two copies of the C allele results in the lowest circulating levels of LDL cholesterol and triglycerides, offering a protective cardiovascular profile [1]. However, the underlying mechanism traps lipids inside liver cells, significantly increasing hepatic fat accumulation [2]. This marked retention leads to a substantially higher risk of non-alcoholic fatty liver disease [3] and alcohol-associated liver cirrhosis [4]. Furthermore, this genotype is linked to an elevated risk of developing type 2 diabetes [5].
Lowest circulating cholesterol levels; Significantly increased risk of fatty liver disease; Higher risk of liver cirrhosis and type 2 diabetes.
Sample genotype: TC (Heterozygous)
This genotype presents a distinct metabolic trade-off due to altered lipid transport. Having one copy of the C allele reduces circulating levels of LDL cholesterol and triglycerides, which generally supports cardiovascular health [1]. However, this reduction occurs because lipids are less efficiently exported from the liver, leading to moderate fat retention in hepatic tissue [2]. This retention increases the risk of developing non-alcoholic fatty liver disease [3]. Additionally, this metabolic shift is associated with a moderately higher susceptibility to type 2 diabetes [4] and liver cirrhosis [5].
Lower circulating LDL cholesterol; Increased risk of liver fat accumulation; Moderately higher risk of type 2 diabetes.
Variants with shared genetic architecture
rs114165349 · ARID1A Gene · Chr 1 · Lipid and Gout Risk
rs2207132 · Chr 20 · Heart Disease Risk
rs2954038 · Chr 8 · Cardiovascular and Liver Health
Biological, clinical and population relevance of 95 loci for blood lipids.
Discovery and refinement of loci associated with lipid levels.
Content updated August 2026.
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