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Updated: Feb 3, 2026

In Silico Clinical Trials for Cardiovascular Disease
Published on: May 27, 2022
Genetic and secondary causes of severe HDL deficiency and cardiovascular disease
Andrew S Geller1,2, Eliana Y Polisecki1, Margaret R Diffenderfer1
1Boston Heart Diagnostics, Framingham, MA 01702.
Insights
Severe HDL deficiency is rare, often caused by secondary factors. Genetic mutations in ABCA1 and APOA1 are linked to the highest rates of atherosclerotic cardiovascular disease (ASCVD).
Area of Science:
- Genetics
- Cardiology
- Biochemistry
Background:
- Severe high-density lipoprotein (HDL) deficiency is a rare condition.
- Understanding its genetic and secondary causes is crucial for managing associated cardiovascular risks.
Purpose of the Study:
- To investigate the secondary and genetic underpinnings of severe HDL deficiency.
- To determine the prevalence of mutations in key lipid-related genes and their association with atherosclerotic cardiovascular disease (ASCVD).
Main Methods:
- A large cohort of 258,252 subjects was screened for severe HDL deficiency (HDL cholesterol <20 mg/dl).
- Subjects with secondary causes or specific conditions were excluded.
- Eligible subjects underwent sequencing of 23 lipid-related genes, including ABCA1, LCAT, APOA1, and LPL.
- Prevalence of ASCVD was compared across genetic mutation groups and a mutation-negative cohort.
Main Results:
- Severe HDL deficiency was identified in 0.33% of men and 0.099% of women.
- Secondary causes accounted for 40.1% of cases.
- Mutations or variants in ABCA1, LCAT, APOA1, or LPL were found in 48.8% of sequenced subjects.
- The highest ASCVD prevalence rates were observed in subjects with ABCA1 (37.0%) and APOA1 (40.0%) mutations.
Conclusions:
- Severe HDL deficiency is uncommon, with a significant proportion attributable to secondary causes.
- Genetic variations in ABCA1, LCAT, APOA1, and LPL play a role in HDL deficiency.
- ABCA1 and APOA1 mutations are strongly associated with increased ASCVD risk in individuals with severe HDL deficiency.
Abstract:
We assessed secondary and genetic causes of severe HDL deficiency in 258,252 subjects, of whom 370 men (0.33%) and 144 women (0.099%) had HDL cholesterol levels <20 mg/dl. We excluded 206 subjects (40.1%) with significant elevations of triglycerides, C-reactive protein, glycosylated hemoglobin, myeloperoxidase, or liver enzymes and men receiving testosterone. We sequenced 23 lipid-related genes in 201 (65.3%) of 308 eligible subjects. Mutations (23 novel) and selected variants were found at the following gene loci: 1) ABCA1 (26.9%): 2 homozygotes, 7 compound or double heterozygotes, 30 heterozygotes, and 2 homozygotes and 13 heterozygotes with variants rs9282541/p.R230C or rs111292742/c.-279C>G; 2) LCAT (12.4%): 1 homozygote, 3 compound heterozygotes, 13 heterozygotes, and 8 heterozygotes with variant rs4986970/p.S232T; 3) APOA1 (5.0%): 1 homozygote and 9 heterozygotes; and 4) LPL (4.5%): 1 heterozygote and 8 heterozygotes with variant rs268/p.N318S. In addition, 4.5% had other mutations, and 46.8% had no mutations. Atherosclerotic cardiovascular disease (ASCVD) prevalence rates in the ABCA1, LCAT, APOA1, LPL, and mutation-negative groups were 37.0%, 4.0%, 40.0%, 11.1%, and 6.4%, respectively. Severe HDL deficiency is uncommon, with 40.1% having secondary causes and 48.8% of the subjects sequenced having ABCA1, LCAT, APOA1, or LPL mutations or variants, with the highest ASCVD prevalence rates being observed in the ABCA1 and APOA1 groups.
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