Author + information
- Ida Surakka, PhDa,b,
- Whitney E. Hornsby, PhDa,b,
- Linda Farhat, MSa,b,
- Melvyn Rubenfire, MDa,b,
- Lars G. Fritsche, PhDa,c,
- Kristian Hveem, MD, PhDd,e,
- Y. Eugene Chen, MD, PhDa,f,
- Robert D. Brook, MDa,b,
- Cristen J. Willer, PhDa,b,g and
- Richard L. Weinberg, MD, PhDa,b,∗ ()
- aUniversity of Michigan, Michigan Medicine, Ann Arbor, Michigan
- bDepartment of Internal Medicine, Division of Cardiovascular Medicine, Michigan Medicine, Ann Arbor, Michigan
- cDepartment of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan
- dK.G. Jebsen Center for Genetic Epidemiology and Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- eHUNT Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway
- fDepartment of Internal Medicine, Michigan Medicine, Ann Arbor, Michigan
- gDepartment of Computational Medicine and Bioinformatics and Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- ↵∗Address for correspondence:
Dr. Richard L. Weinberg, 1500 East Medical Center Drive, SPC 5853, Cardiovascular Center Room 2713, Ann Arbor, Michigan 48109.
A novel frameshift variant was identified in APOB that segregates in a dominant manner with low levels of low-density lipoprotein cholesterol. Affected family members show no apparent clinical complications. There is no consensus regarding clinical management, and the long-term consequences of low levels of low-density lipoprotein cholesterol remain unknown. (Level of Difficulty: Advanced.)
A 20-year-old Caucasian male patient presented to his primary care provider with complaints of palpitations. His 12-lead electrocardiogram was normal. A lipid profile revealed a low-density lipoprotein cholesterol (LDL-C) level of 8 mg/dl. The patient was referred to the Michigan Medicine Lipid Disorders Clinic for evaluation. His physical examination was notable for a weight 64 kg, height 180 cm, and body mass index 19.5 kg/m2. The remainder of his physical examination was unremarkable, including no evidence of hepatomegaly, peripheral neuropathy, or retinopathy. A lipoprotein metabolism profile (Mayo Clinic, Rochester, Minnesota) revealed total cholesterol 77 mg/dl, LDL-C 15 mg/dl, high-density lipoprotein cholesterol 48 mg/dl, triglycerides 32 mg/dl, and apolipoprotein B (ApoB) 15 mg/dl. Thyroid-stimulating hormone level, comprehensive metabolic panel, and complete blood count were normal.
• To understand that genetic testing may be necessary for diagnostic accuracy when encountering patients with low levels of LDL-C.
• To understand the causes of low levels of LDL-C and how to manage patients with genetic conditions that cause low levels of LDL-C.
Past Medical History
The patient’s childhood development was normal, with no reported history of failure to thrive; no symptoms of malabsorption; and no neurological, hepatic, or visual abnormalities. There was no history of chronic or acute infections, recent hospitalizations, or inflammatory disease.
Causes of very low levels of LDL-C are listed in Table 1. Based on the history and available data, the etiology of this patient’s very low LDL-C was hypothesized to be genetic (1,2). Genetic conditions causing very low LDL-C levels have varied etiologies and clinical presentations (3). They are characterized by plasma levels of total cholesterol, LDL-C, and apoB <5th percentile, with typical LDL-C values between 20 and 50 mg/dl (4). Homozygous or biallelic pathogenic mutations in genes encoding key proteins in lipoprotein metabolism and synthesis cause abetalipoproteinemia, homozygous familial hypobetalipoproteinemia (FHBL), and chylomicron retention disease. These diseases typically present with prominent multiorgan system phenotypes identified in infancy or youth, including failure to thrive, steatorrhea, and fat-soluble vitamin deficiencies often with retinopathy, neuropathy, or coagulopathy (4).
This patient lacked any of the multiorgan system dysfunction of abetalipoproteinemia, homozygous FHBL, or chylomicron retention disease despite having an LDL-C <5th percentile. Thus, other genetic causes of low LDL-C, which typically have little or no clinical manifestations, were considered (Figure 1). These included heterozygous or homozygous familial hypolipoproteinemia due to mutations in PCSK9 and heterozygous FHBL due to mutations in APOB (Figure 1) (2). Heterozygous FHBL is the most common cause of LDL-C <5th percentile, with an estimated prevalence of APOB-related FHBL of 1 in 1,000 to 3,000 (4,5). However, this patient presented with an LDL-C of 8 mg/dl, which is much lower than typical for heterozygous FHBL, thereby confounding the clinical picture. Contrarily, patients with homozygous or compound heterozygous FHBL have LDL-C levels and clinical conditions similar to the severe recessive disorders (i.e., abetalipoproteinemia).
Cascade screening for low levels of LDL-C was performed for first- and second-degree relatives. Next, the index patient and 7 family members (Table 2, Figure 2) enrolled into the Cardiovascular Health Improvement Project, a longitudinal biorepository (HUM00052866). Saliva samples were collected, coded, and linked to electronic health records, and DNA was isolated. High-coverage whole genome sequencing (30×) was performed by Psomagen, Inc. (Rockville, Maryland). Supplemental Table 1 and the Supplemental Material provide a summary of genetic sequencing data and methods.
Whole genome sequencing
Of the rare (not present in gnomAD  or 1000 Genomes European reference populations  or minor allele frequency <1%) high-impact polymorphisms (variant effect predictor annotations as transcript ablation, splice acceptor or donor, stop gained, frameshift, and stop or start lost) identified in the 8 samples, only 1 (APOB p.Val853fs) followed the dominant inheritance pattern with the low LDL-C status (Table 3, Figure 3). All 5 affected cases carried 1 copy of the rare mutation, and 3 unaffected control subjects carried none (LOD score = 1.51).
A similar analysis was performed for moderate-impact mutations (missense, inframe insertion and deletion, and protein altering). A total of 7 mutations were identified that showed a dominant mode of inheritance with low LDL-C. None of these 7 mutations fell into genes known to affect lipid metabolism (Table 3, Figure 3).
The identified APOB frameshift variant was not present in any of the public databases, and we were not able to find any publications or case reports in the published data. Thus, we believe that this particular variant is novel. There are multiple previously published mutations in APOB shown to cause low LDL-C levels, but also observed in conjunction with adverse liver effects including hepatic steatosis and hepatocellular carcinoma (1,4,8). The LDL-C levels seen for the affected cases (undetectable and between 8 and 19 mg/dl) are significantly lower (T-statistic for the difference in mean = 7.58, 2-tailed p = 3.0 × 10−8) than the average LDL-C level of heterozygous APOB loss-of-function (LoF) mutation carriers in the HUNT (9) biobank (mean LDL-C for APOB LoF carriers = 56 mg/dl) (Figure 4). The extreme LDL-C phenotype (LDL-C values <10 mg/dl) observed could be attributable to an uncharacterized property of this particular mutant ApoB protein or an unidentified genetic cause, including an unknown genetic variant or the possibility of a polygenic burden for low LDL-C levels.
Patients with heterozygous APOB-related FHBL have been reported to have elevated levels of liver enzymes. Decreased secretion of mutated apoB from the liver results in reduced hepatic triglyceride export, which can lead to the development of hepatic steatosis, oral fat intolerance, and intestinal fat malabsorption (4,10). There have also been reports of patients with APOB-related FHBL developing cirrhosis and hepatocellular carcinoma (4,8,11). Thus, despite having normal liver function, it was recommended that the index patient and affected family members obtain liver ultrasounds and have liver enzymes measured as part of routine medical care. Additional testing including retinal examinations and serum fat-soluble vitamin levels (e.g., vitamin A) as well as formal testing for peripheral neuropathy was recommended. The patient was counseled that offspring should have lipid profiles by age 2 years, and should consult with a lipid specialist if LDL-C is <5th percentile (3).
Discussion of Heterozygous APOB-Related FHBL
The novel finding is that the identified APOB LoF variant carriers have significantly lower LDL-C levels compared with levels of the carriers from the HUNT study. Moreover, the index patient and affected family members were without known adverse clinical complications. Hepatic steatosis and elevation of liver enzymes are the main clinical manifestations (4); however, the current screening approaches, liver ultrasound and fibroscan, lack sensitivity, and subclinical disease can progress. Genetic testing is important for risk-stratifying patients into groups requiring long-term and routine follow-up, such as those with APOB LoF compared with PCSK9 LoF variant carriers, the latter of which typically do not have any adverse clinical manifestations.
The index patient and affected cases were not clinically followed after the management plan was discussed due to the proximity of residence to clinic location.
This case report is reflective of a family with normal development without known adverse clinical complications despite very low levels of LDL-C. Given the finding of an APOB LoF as the cause for the low LDL-C, routine screening for liver disease and other associated compilations should be pursued long-term. Importantly, this patient and affected family members had normal development with very low LDL-C levels, and will likely gain protection against atherosclerotic cardiovascular disease.
Dr. Willer is supported by National Institutes of Health grants R01-HL127564, R35-HL135824, R01-HL142023, R01-HL-109942, and R01-HL109946; and her spouse works for Regeneron. All other authors have reported that they have no relationships relevant to the contents of this paper to disclose.
The authors attest they are in compliance with human studies committees and animal welfare regulations of the authors’ institutions and Food and Drug Administration guidelines, including patient consent where appropriate. For more information, visit the JACC: Case Reports author instructions page.
- Abbreviations and Acronyms
- apolipoprotein B
- familial hypobetalipoproteinemia
- low-density lipoprotein cholesterol
- Received January 8, 2020.
- Revision received March 9, 2020.
- Accepted March 18, 2020.
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