Cholesterol & Lipoproteins

3'UTR variant in ABCG1 that may reduce transporter expression, impairing cholesterol efflux to HDL and increasing susceptibility to coronary artery disease.

Intronic SCARB1 variant associated with altered HDL-receptor function, subclinical atherosclerosis, and increased coronary heart disease risk

Intronic variant in SCARB1 that affects SR-BI receptor function and the intestinal and hepatic uptake of fat-soluble vitamin E (alpha-tocopherol) and carotenoids from HDL particles

Intronic variant in SCARB1 that tags a haplotype affecting SR-BI receptor-mediated uptake of macular carotenoids (lutein, zeaxanthin) and beta-carotene from HDL particles; T allele carriers show up to 24% higher serum lutein per allele

Upstream regulatory variant in CYP7A1 that tags haplotypes affecting bile acid synthesis rate and LDL cholesterol clearance

Promoter insertion variant in APOC1 that increases gene transcription by 50%, raising apolipoprotein C-I levels and strengthening CETP inhibition to produce higher HDL-cholesterol and lower triglycerides.

Intronic regulatory variant that increases DAB2 expression in kidney tubules, amplifying TGF-β-driven fibrosis and raising chronic kidney disease risk

Nonsense mutation in APOB creating a premature stop codon at position 1333, truncating apolipoprotein B-100 to ~30% of its normal length and causing familial hypobetalipoproteinemia with very low LDL cholesterol; pathogenic for FHBL

Frameshift deletion in APOB causing truncated apolipoprotein B-100, reducing LDL production and impairing fat-soluble vitamin absorption; pathogenic for familial hypobetalipoproteinemia

Frameshift deletion in APOB that truncates apolipoprotein B, causing familial hypobetalipoproteinemia — very low LDL cholesterol with cardiovascular protection but hepatic steatosis risk

Nonsense mutation in APOB creating a premature stop codon at position 2085, producing a truncated apolipoprotein B fragment (ApoB-46) that reduces LDL and VLDL secretion; pathogenic for familial hypobetalipoproteinemia type 1

Single-nucleotide deletion in APOB creating a truncated apolipoprotein B (ApoB-67) — carriers have dramatically reduced LDL and total cholesterol with strong cardiovascular protection, but face risk of hepatic steatosis and fat-soluble vitamin deficiency

Nonsense variant creating a premature stop codon at amino acid 2279 of apolipoprotein B-100, producing a severely truncated apoB-50 protein and causing familial hypobetalipoproteinemia type 1 with markedly reduced LDL cholesterol and hepatic steatosis risk

Nonsense mutation producing a severely truncated apolipoprotein B (apoB-32) that cannot be secreted as VLDL or LDL, causing familial hypobetalipoproteinemia with very low LDL cholesterol and hepatic steatosis

Nonsense mutation truncating apolipoprotein B at residue 2522, causing familial hypobetalipoproteinemia with characteristically low LDL-C, hepatic steatosis, and potential fat-soluble vitamin insufficiency in heterozygous carriers

Rare APOB stop-gain variant that truncates apolipoprotein B to ~27% of its full length, causing familial hypobetalipoproteinemia with very low LDL-C, hepatic steatosis risk, and fat-soluble vitamin malabsorption in the heterozygous state

Upstream promoter variant in CETP that tags the HDL-raising haplotype block — C allele carriers have lower HDL cholesterol through modestly increased CETP-mediated cholesterol transfer from HDL to VLDL

Intronic ABCA1 variant associated with population differences in HDL cholesterol capacity; the A allele tags reduced cholesterol efflux activity and lower HDL in carriers

Rare APOB missense variant reducing LDL-receptor binding affinity by ~40-50%, classified as a variant of uncertain significance for familial-defective apolipoprotein B

Nonsense mutation in the LDLR gene creating a premature stop codon at position 408, abolishing LDL receptor production and causing familial hypercholesterolemia with severely elevated LDL cholesterol and early cardiovascular disease risk

Intronic variant in CYP7A1 that tags a haplotype block influencing cholesterol 7α-hydroxylase expression; CC homozygotes show elevated LDL-cholesterol and increased subclinical atherosclerosis risk across multiple population studies

CETP promoter variant that reduces CETP expression via Sp1/Sp3 repression, raising HDL cholesterol by ~3–6 mg/dL in A allele carriers

Gain-of-function missense variant in PCSK9 that increases intracellular LDL receptor degradation, causing autosomal dominant familial hypercholesterolemia

Missense variant in the master cholesterol transcription factor SREBP-2 that alters the SCAP-binding regulatory domain and is associated with cardiovascular disease risk and altered cholesterol homeostasis.

Intronic ABCG1 variant near the promoter region; homozygous carriers of the minor A allele showed a 36% lower odds of coronary artery disease in a Chinese Han cohort, suggesting a modest protective effect linked to the ABCG1 cholesterol efflux locus.

Intronic ABCA1 variant associated with lower HDL-cholesterol susceptibility and coronary heart disease risk at one of the most replicated lipid GWAS loci

Intronic ABCA1 variant associated with HDL-C levels under a recessive model; AA homozygotes show measurably different cholesterol efflux capacity and face a heightened risk of adverse outcomes when HDL-C is abnormal

Synonymous coding variant in ABCA1 that tags a regulatory element influencing transporter expression; the common G allele associates with the population-average HDL baseline, while the rare T allele associates with modestly higher HDL-cholesterol

Pathogenic LDLR missense variant abolishing LDL receptor surface expression, causing familial hypercholesterolemia with severely elevated LDL-C from birth

Pathogenic LDLR missense variant in the EGF precursor domain causing familial hypercholesterolemia with severely elevated LDL-C and early cardiovascular disease

Pathogenic LDLR missense variant (p.Tyr828Cys) that traps LDL receptors outside coated pits, causing familial hypercholesterolemia with severely elevated LDL-C and early-onset cardiovascular disease

Intronic HMGCR variant that modulates alternative splicing of exon 13, producing a truncated Δ13 isoform that reduces statin-binding capacity and attenuates LDL-cholesterol lowering in response to statin therapy

Intronic HMGCR variant that tags a haplotype influencing exon 13 alternative splicing — affecting HMGCR enzyme activity, baseline LDL-C levels, and the magnitude of statin-induced LDL reduction

Intronic ABCA1 variant — the C allele tags a liver enhancer that boosts ABCA1 expression, raising HDL-cholesterol; T-allele homozygotes show modestly lower HDL and elevated cognitive decline risk

Intronic ABCA1 variant influencing HDL-cholesterol levels through altered ABCA1 expression; the A allele is associated with modestly reduced HDL.

Lipid metabolism and Alzheimer's risk - E4 carriers respond worse to high saturated fat

CETP promoter variant that raises HDL cholesterol by reducing cholesteryl ester transfer protein activity; A allele carriers show higher HDL-C but mixed cardiovascular outcome evidence.

Intronic variant in the brain cholesterol 24-hydroxylase gene; C allele associated with a higher 24S-hydroxycholesterol/cholesterol ratio in CSF and modestly elevated Alzheimer's disease risk, primarily in East Asian populations

Intronic APOB variant where the A allele (plus strand) is associated with approximately 2-fold increased bile duct cancer risk in men; the G allele is common in East Asian populations and carries no elevated biliary risk

Synonymous variant that reduces SR-BI receptor expression and impairs HDL cholesterol uptake by the liver, lowering HDL-C levels and modestly increasing cardiovascular risk

Pathogenic APOB splice acceptor variant causing familial hypobetalipoproteinemia — heterozygous carriers have ~50% lower LDL-C and apoB, conferring cardiovascular protection but requiring liver and fat-soluble vitamin monitoring

Second component of the APOL1 G1 kidney disease risk haplotype — a missense variant that, together with rs73885319 (S342G), confers 7- to 29-fold increased risk for non-diabetic CKD under a recessive inheritance model in African-ancestry populations

Intronic APOB variant associated with modest differences in apolipoprotein B levels, cardiovascular risk, and ischemic stroke susceptibility across populations.

Six-base-pair in-frame deletion removing two amino acids from apolipoprotein L1, conferring trypanosome resistance but dramatically increasing chronic kidney disease risk in homozygous or compound heterozygous state with G1

APOL1 G1 kidney disease risk variant — missense change that evolved for trypanosome resistance but causes nephropathy in the recessive state

APOE E2 variant - generally protective for cardiovascular health

Intronic variant in the rate-limiting bile acid synthesis gene; T allele carriers show reduced LDL-lowering response to statins and elevated cardiovascular risk.

3' UTR variant in SCARB1 that tags a haplotype with reduced SR-BI expression in the liver, lowering HDL cholesterol and impairing reverse cholesterol transport efficiency