Skip to main content
PLOS One logoLink to PLOS One
. 2026 Apr 20;21(4):e0344627. doi: 10.1371/journal.pone.0344627

Genetic testing in individuals with extreme HDL-C levels: Diagnostic yield and clinical implications from the Tromsø Study

Åsa Schawlann Ølnes 1,2,‡,*, Marianne Teigen 1,2,, Thea Bismo Strøm 1, Erik Kristoffer Arnesen 3, Antoine Rimbert 4, Anne Elise Eggen 5, Katrine Bjune 1
Editor: Chiara Pavanello6
PMCID: PMC13095017  PMID: 42008427

Abstract

Aim

This study aimed to assess the prevalence of genetic variants responsible for extreme levels of high-density lipoprotein cholesterol (HDL-C) and evaluate the adequacy of current thresholds for genetic testing of HDL-related dyslipidemia.

Methods

Using data from the Tromsø Study, a population-based cohort in Northern Norway, we identified 210 individuals with HDL-C levels ≤ 0.5 mmol/L or ≥ 3.0 mmol/L. Six HDL-related genes (ABCA1, APOA1, CETP, LCAT, PLTP, SCARB1) were sequenced in these participants. We classified variants according to ACMG guidelines, incorporating functional assays and UK Biobank data for additional phenotype-genotype associations.

Results

We identified 38 variants of interest across six HDL-related genes, of which 10 were considered potentially causative, found in 14 individuals. Genetic causes were detected in 33.3% of individuals with low HDL-C and 5.05% of those with high HDL-C. Sex-specific analyses showed that using HDL-C thresholds aligned with population distributions improved detection of individuals with pathogenic variants, particularly among women with high HDL-C and men with low HDL-C. These findings suggest that current uniform thresholds may overlook clinically relevant cases and that incorporating sex-specific HDL-C distributions could enhance the identification of individuals with suspected genetic HDL disorders.

Conclusions

Genetic testing for HDL-related dyslipidemia is underutilized, with many individuals not meeting the current extreme HDL-C threshold criteria. Revised sex-specific thresholds for genetic testing will improve the identification of pathogenic variants and provide more accurate diagnoses of HDL-related disorders. Continued research is essential to refine our understanding of HDL genetics and its clinical implications.

Introduction

The strong observational inverse association between high-density lipoprotein cholesterol (HDL-C) levels and cardiovascular disease (CVD) risk has, over the last two decades, encouraged several therapeutic efforts to increase HDL-C levels [1,2]. Whereas previous trials have failed to deliver the expected protective effects against CVD, the focus of the new generation components has shifted from increasing the atheroprotective HDL-C levels to decreasing the atherogenic apolipoprotein B-containing lipoproteins [37]. Furthermore, while HDL-C is often referred to as “good cholesterol” in clinical contexts, recent population studies have raised concerns that exceptionally high HDL-C levels may paradoxically be linked to increased mortality, underscoring the complexity of HDL dynamics [811].

HDL plays a crucial role in reverse cholesterol transport, the transport of cholesterol from peripheral tissues to the liver for excretion. The biogenesis of HDL begins with the ATP-binding cassette transporter A1 (ABCA1), which effluxes cellular phospholipids and cholesterol to apolipoprotein A1 (ApoA1), forming nascent discoidal pre-β-HDL [12]. This precursor is subsequently converted into mature spherical α-HDL through the action of lecithin-cholesterol acyltransferase (LCAT), which esterifies free cholesterol within the discoidal HDL, allowing it to be sequestered in the core and creating a more spherical HDL particle [13].

As HDL matures and accumulates cholesterol, it becomes a substrate for both cholesteryl ester transfer protein (CETP) and phospholipid transfer protein (PLTP). CETP mediates the exchange of cholesteryl esters and triglycerides between HDL and low-density lipoprotein (LDL) or very-low-density lipoprotein (VLDL), transferring cholesteryl esters from HDL to these particles and triglycerides in the opposite direction. In contrast, PLTP primarily mediates the transfer of phospholipids between lipoproteins [14,15]. These processes contribute to HDL size heterogeneity and are key mechanisms in the redistribution of cholesterol among lipoproteins, also facilitating hepatic cholesterol uptake via the LDL receptor. Additionally, cholesterol from HDL is returned to the liver through other pathways, such as via the hepatic scavenger receptor class B type 1 (SR-B1), enabling the liver to recycle or excrete cholesterol [16].

Variants in genes associated with reverse cholesterol transport play a significant role in determining HDL-C levels. These genes influence various stages of HDL metabolism, and extreme HDL-C levels have been linked to notable cardiovascular health implications in affected individuals [9,17,18]. In Norway, patients with extreme HDL-C levels (≤ 0.5 mmol/L or ≥ 3 mmol/L) have been offered genetic testing of the five key genes ABCA1, APOA1, CETP, LCAT and SCARB1 (encoding SR-B1). At the Unit for Cardiac and Cardiovascular Genetics, Oslo University Hospital, approximately 270 individuals have been assessed over the past 25 years, primarily referred to us due to personal or family history of heart disease or dyslipidemia. In comparison, more than 70 000 patients with abnormal LDL cholesterol (LDL-C) levels have been analyzed in the same period. Patient numbers were based on data from our diagnostic clinic that have not been previously published. While familial hypercholesterolemia is estimated to affect approximately 1 in 300 individuals in the general population, genetic testing for HDL-related disorders remains rare, resulting in an unclear understanding of the prevalence of inherited HDL deficiencies [19]. Further, despite extensive population studies on HDL-related genes, functional analyses of identified variants are limited, leaving a gap in our understanding of the genotype-phenotype relationship [20].

Due to infrequent clinical referrals of HDL-related dyslipidemia and potentially under-examined phenotype caused by the rarity of individuals with extreme HDL-C levels, we have in this study utilized one of the large Norwegian health surveys to evaluate the health care offered to these patients in Norway. In collaboration with the Tromsø Study, we identified individuals with HDL-C ≤ 0.5 mmol/L or ≥ 3 mmol/L, and analyzed ABCA1, APOA1, CETP, LCAT, PLTP and SCARB1 for disease causing variants in these individuals. While PLTP is not part of the current diagnostic gene panel at our unit, it was included because the same experimental system used for functional characterization of CETP variants was applicable to PLTP, allowing parallel assessment. Given the limited functional data available for PLTP and its established role in HDL metabolism, we considered this an opportunity to explore the contribution of this gene to extreme HDL-C phenotypes. Further, we assessed all variants found according to the guidelines from the American College of Medical Genetics and Genomics and The Association for Molecular Pathology (ACMG/AMP; hereafter referred to as ACMG) [21,22], applying functional protein-specific characterization and clinical data from the UK Biobank. While the findings of this study reinforce the rarity of monogenic causes of extreme HDL-C levels, they have also led us to modify the criteria for genetic testing of HDL-related dyslipidemia to alleviate sex discrimination in our clinic.

Materials and methods

Study population and design

The Tromsø Study, established in 1974, is an ongoing population-based multipurpose health study of adults in the municipality of Tromsø in Northern Norway [23]. Seven data collections have been implemented between 1974 and 2016, and the eighth wave of the Tromsø Study is ongoing. Due to limited biological material available from the first three surveys, we used data from the fourth (Tromsø-4, 1994–1995, n = 27 158), fifth (Tromsø-5, 2001, n = 8 130), sixth (Tromsø-6, 2007–2008, n = 12 984) and seventh survey (Tromsø-7, 2015–2016, n = 21 083) for this project. The participant inclusion criteria were HDL-C levels ≤ 0.5 mmol/L or ≥ 3.0 mmol/L in at least one participation. These stringent thresholds were historically selected in clinical settings to enrich for individuals with a high likelihood of monogenic causes of extreme HDL-C levels, at a time when sequencing capacity and costs limited broader genetic screening. Importantly, individuals with known monogenic disorders affecting HDL metabolism have been shown to present with HDL-C levels within these ranges, supporting the biological relevance of the applied cutoffs [2426]. Cholesterol levels from all participations were obtained to monitor the normal fluctuation in individual lipid profiles. The biological material obtained was DNA, and the extension of the sequencing analyses performed was dependent on the availability of the biological material.

Authorizations

This research project was approved by the Tromsø study Data and Publication Committee (Project 8030.00457) and by the Regional Committee for Medical Research Ethics – South East (Application 142265). The study was conducted according to the Declaration of Helsinki. Written informed consent was collected by the Tromsø Study from all participants. The samples and data were accessed for this research project on 03.05.2022.

Numbering of nucleotides and codons

The following transcripts were used: ABCA1, NM_005502.4; APOA1, NM_000039.3; CETP, NM_000078.3; LCAT, NM_000229.2; PLTP, NM_006227.4; SCARB1, NM_005505.5. Codon number 1 was defined as the ATG start codon, with the A of the start codon set as nucleotide number 1. The genetic variants at protein level are noted with prefix p. throughout the manuscript.

UK Biobank study and whole exome sequencing data

The UK Biobank study, described in detail previously, is a population-based prospective cohort conducted in the United Kingdom in which > 500 000 individuals aged 40–69 years were included from 2006 to 2010 [27]. The study has been approved by the North West Multi-Centre Research Ethics Committee for the United Kingdom, from the National Information Governance Board for Health and Social Care for England and Wales, and by the Community Health Index Advisory Group for Scotland. The present research has been conducted using the UKBB resource under the application number 49823. The records of individuals who have withdrawn from UKBB were removed from the analyses. Genetic variants in genes of interest were screened using whole-exome sequencing (WES) data from the UK Biobank. WES sequencing technical and analytic details have been reported previously [28]. In short, WES was performed using IDT xGen Exome Research Panel v1.0, targeting 38 997 831 bases in 19 396 genes. Exomes were captured including 100 bp flanking regions. Among participants we focused on 469 835 individuals for whom WES data was available. Variant filtering (GRCh38) was performed using vcf files (format VCFv4.2) with bcftools (v1.14) and jvarkit [29,30]. Genetic and phenotypic data were combined and processed using RStudio (v.2022.02.1).

DNA sequencing and variant classification

DNA was analyzed by standardized accredited Sanger sequencing. Oligonucleotide sequences used for PCR amplification are available upon request. Genetic variants were assessed according to the ACMG guidelines, categorizing variants based on their pathogenic potential as benign (class 1), likely benign (class 2), uncertain significance (class 3), likely pathogenic (class 4) or pathogenic (class 5) [21,31]. The filtering allele frequency cutoffs for the benign criteria BA1 and BS1 were set at ≥ 0.005 and ≥ 0.002, respectively, while for the pathogenic PM2 criterion, the maximum allele frequency cutoff was ≤ 0.0002 [32]. For CETP variants with the highest allele frequency in the East Asian population, the second highest allele frequency among the populations in the Genome Aggregation Database (gnomAD v.4.1.0) was evaluated for the BA1/BS1 criteria, due to the frequency of increased HDL-C in the Japanese population [33]. The pathogenic phenotype criterion PP4 was applied as strong evidence when variants were identified in individuals with HDL-C ≤ 0.1 mmol/L or with Tangier disease, LCAT deficiency or Fish-eye disease, or for loss-of-function characterization in patient material from the literature.

Functional assays and distribution of HDL-C levels

Methods and results from HDL-C distribution and functional assays characterizing variants in ABCA1, CETP, LCAT and SCARB1 can be found in S1 File.

Statistical analyses

Data are presented as mean (± standard deviations (SD)) unless otherwise stated. GraphPad Prism 10.1.2 (GraphPad Software LLC, Boston, MA) was used to calculate p values by an ordinary one-way ANOVA followed by Dunnett’s multiple comparisons test. Effect sizes were calculated using Hedges’ g in Microsoft Excel. A positive value of g indicates higher activity in the variant compared to the wild-type, while a negative value indicates reduced activity. A significance level of p < 0.05 was used.

Results

Participants in the Tromsø Study with HDL-C levels ≤ 0.5 mmol/L or ≥ 3 mmol/L

In line with current thresholds for HDL-related genetic testing in Norway, we screened the Tromsø Study for participants with HDL-C levels at the extreme ends of the distribution. Across the Tromsø-4 to Tromsø-7 surveys, conducted between 1994 and 2016, a total of 36 626 unique individuals participated. Of these, 210 participants (0.57%) had at least one recorded HDL-C measurement of ≤ 0.5 mmol/L or ≥ 3 mmol/L (Fig 1). Specifically, 198 individuals (0.54%) had HDL-C levels exceeding 3 mmol/L (high HDL-C group), while 12 individuals (0.033%) had HDL-C levels of 0.5 mmol/L or lower (low HDL-C group). Several participants were involved in multiple surveys, and 165 of the 210 individuals had more than one HDL-C measurement available. On group level, utilizing all available measurements for each individual, the average HDL-C levels for the low and high HDL-C groups were 0.57 mmol/L and 2.87 mmol/L, respectively.

Fig 1. Overview of the four Tromsø Studies included in this article.

Fig 1

The figure depicts the number of participants, sex distribution, and age range for each survey. Across all four studies, a total of 36 626 unique individuals were included. Among these, only 210 participants had at least one extreme HDL-C measurement – defined as ≤ 0.5 mmol/L (n = 12) or ≥ 3.0 mmol/L (n = 198). Participants were sequenced in six HDL-related genes (ABCA1, APOA1, CETP, LCAT, PLTP, SCARB1). Created using BioRender.

While individual lipid profiles typically fluctuate, dyslipidemia caused by monogenic factors generally results in a consistent abnormal lipid profile across multiple measurements over time [34]. The average HDL-C levels for the included participants varied significantly, particularly for the high HDL-C group (S1 Table). Furthermore, the proportion of individuals with high HDL-C levels (≥ 3 mmol/L) varied across the four surveys: 0.13% in Tromsø-4 (35/27 158), 0.17% in Tromsø-5 (14/8 130), 0.32% in Tromsø-6 (42/12 984), and 0.65% in Tromsø-7 (137/21 083). This represents a fivefold increase in the proportion of individuals with extremely high HDL-C levels in Tromsø-7 compared to Tromsø-4, and roughly double the proportion seen in Tromsø-6. Whether this variation is attributable to demographic changes such as increasing participant age in later surveys, or due to systematic differences in HDL-C measurement methods over time, remains uncertain.

While genetic dyslipidemia is primarily autosomally inherited, a sex segregation between the two groups was suspected based on sex-adjusted HDL-C reference limits. Accordingly, all but one of the individuals with low HDL-C levels were men, while 83% (164 of 198) in the high HDL-C group were women. This sex discrimination is in accordance with the findings in a similar study by Sadananda et al. of 80% and 26% male in low and high HDL-C group, respectively [35].

Sex-specific distributions of HDL-C in a large clinical dataset further demonstrated marked differences between men and women (S1 Fig). Using current extreme HDL-C thresholds (≤ 0.5 mmol/L and ≥ 3.0 mmol/L), only a very small fraction of the population was captured, with clear sex imbalance. Among men, 0.03% had HDL-C ≤ 0.5 mmol/L and 0.03% had HDL-C ≥ 3.0 mmol/L, whereas among women, 0.01% had HDL-C ≤ 0.5 mmol/L and 0.15% had HDL-C ≥ 3.0 mmol/L.

Variants of interest identified in subjects at the extreme ends of the HDL-C distribution

DNA from all 210 participants in both the high and low HDL-C groups were sequenced for variants in six major HDL-related genes: ABCA1, APOA1, CETP, LCAT, PLTP and SCARB1. In total, 38 heterozygous distinct variants of interest including all missense and promoter variants, as well as synonymous and intronic variants predicted to affect mRNA splicing, were found across the six genes: ABCA1 (n = 12), APOA1 (n = 4), CETP (n = 11), LCAT (n = 3), PLTP (n = 3) and SCARB1 (n = 5) (Table 1). A complete list of additional variants detected in the cohort is available in S2 and S3 Tables.

Table 1. Variants of interest identified in extreme HDL-C phenotype.

Protein Nucleotide Phenotype Tromsø [HDL-C] n (%) Functional assay ACMG Class Relative HDL-C
UK biobank % (n)
High Low % of WT (SD) References
ABCA1
 p.R219K c.656G > A 86 (43.4%) 6 (50%) 90% (± 7) [36] 1 −0.21% (195 930)
 p.S296T c.886T > A 1 (0.5%) 98% (± 11) S2 Fig 2 −4.63% (18)
 p.V771M c.2311G > A 11 (11.1%) 2 (16.7%) 85% (± 14) [36] 1 2.39% (24 913)
 p.V825I c.2473G > A 25 (12.6%) 2 (16.7%) 97% (± 7) S2 Fig 1 1.62% (50 059)
 p.I883M c.2649A > G 37 (18.7%) 2 (16.7%) 84% (± 8) [37] 1 1.18% (104 371)
 p.C887F c.2660G > T 2 (1%) 87% (± 9) [37] 1 −4.12% (66)
 p.E1172D c.3516G > C 12 (6.1%) 1 (8.3%) 74% (± 9) [37] 1 1.37% (26 132)
 p.S1181F c.3542C > T 1 (0.5%) 69% (± 19) [37] 3 −4.97% (1429)
 p.K1587R c.4760A > G 132 (66.7%) 4 (33.3%) 106% (± 5) [36] 1 1.66% (380 842)
 p.V1674I c.5020G > A 2 (1%) 77% (± 10) S2 Fig 1 −2.20% (111)
 p.G1818E c.5453G > A 2 (16.7%) 31% (± 10) S2 Fig 4 −32.75% (4)
 p.R1925Q c.5774G > A 4 (2%) 100% (± 12) [37] 2 4.05% (547)
CETP
 p.A15G c.44C > G 3 (1.5%) 121% (± 23) [38] 1 8.94% (1481)
 p.D131N c.391G > A 1 (0.5%) 64% (± 23) [38] 3 11.43% (61)
 p.L290P c.869T > C 1 (0.5%) 3% (± 4) S3 Fig 3 20.72% (182)
 p.Q337X c.1009C > T 4 (2%) 2% (± 3) S3 Fig 5 −16.01% (1)
 p.V385M c.1153G > A 1 (0.5%) 81% (± 12) S3 Fig 2 0.05% (1296)
 p.A390P c.1168G > C 9 (4.5%) 1 (8.3%) 228% (± 50) [38] 1 −6.84% (42 886)
 p.V422I c.1264G > A 171 (86.4%) 8 (66.7%) 110% (± 25) [38] 1
 p.E443K c.1327G > A 1 (0.5%) 18% (± 6) [38] 3 25.27% (18)
 p.D459G c.1376A > G 1 (0.5%) 19% (± 11) [38] 5 7.75% (158)
 p.R468Q c.1403G > A 3 (1.5%) 1 (8.3%) 73% (± 9) [38] 1 −7.22% (30 414)
 Intron c.1321 + 1G > A 1 (0.5%) r.1249_1321del, fsTer4a S3 Fig 5 25.52% (29)
LCAT
 p.S232T c.694T > A 7 (3.5%) 3 (25%) 84% (± 9) S4 Fig 1 −1.78% (26 000)
 p.M276K c.827T > A 2 (16.7%) 2% (± 3) S4 Fig 5
 p.E378K c.1132G > A 1 (0.5%) 57% (± 6) S4 Fig 3 −4.55% (164)
SCARB1
 p.G2S c.4G > A 28 (14.1%) 1 (8.3%) 103% (± 7) S5 Fig 1 −0.23% (76 978)
 p.G12R c.34G > A 1 (0.5%) 100% (± 7) S5 Fig 3 −0.89% (1)
 p.V135I c.403G > A 1 (0.5%) 61% (± 7) S5 Fig 1 −1.24% (9667)
 p.I231V c.691A > G 1 (0.5%) 69% (± 8) S5 Fig 3
 Silent c.591C > T 1 (0.5%) r.590_630del, fsTer34a S5 Fig 3
APOA1
 Promoter c.-12C > T 1 (8.3%) 3
 p.E100Q c.298G > C 1 (0.5%) 3 4.09% (2)
 p.R184L c.551G > T 1 (8.3%) 4
 p.A188S c.562G > T 2 (1%) 3 −0.72% (849)
PLTP
 p.E211Q c.631G > C 3 (1.5%) 3 9.66% (69)
 p.R380W c.1138C > T 2 (1%) 3 0.69% (867)
 p.V422M c.1264G > A 2 (1%) 3

Missense and promoter variants, as well as synonym and intronic variants predicted by SpliceAI to affect mRNA splicing, in the genes ABCA1, APOA1, CETP, LCAT, PLTP and SCARB1 from 210 participants with extreme HDL-cholesterol (HDL-C) levels in the Tromsø Study. All variants found are listed in S2 and S3 Tables. For each variant, the table provides the amino acid change (missense variants), nucleotide change, the number and percentage of carriers in the high and low HDL-C groups from the Tromsø Study (Phenotype Tromsø [HDL-C]), results from functional assays compared to wild-type, and references to where the assays were performed (S2S6 Figs). Variants are classified according to the guidelines from The American College of Medical Genetics and Genomics and The Association for Molecular Pathology (ACMG) as class 1 (benign), class 2 (likely benign), class 3 (variant of uncertain significance), class 4 (likely pathogenic), or class 5 (pathogenic), with classification criteria outlined in S2 and S3 Tables. The final column includes UK Biobank data, showing the number of individuals carrying each variant and the corresponding percentile change in HDL-C levels relative to the population average.

SD: standard deviation. aFunctional activity given as effect of variant on RNA level and position of frameshift-induced stop codon.

For missense and splice variants of interest, functional characterization was performed utilizing protein specific activity assays (ABCA1, CETP, LCAT and SCARB1) or minigene assay, respectively (S2–S5 Figs, Table 1). Additionally, qPCR analyses showed no differences in transfection efficiency between constructs (S6 Fig). Most tested variants demonstrated functional activity comparable to wild-type, consistent with benign or likely benign classification. In contrast, marked loss of function was observed for a limited number of variants. These included the novel ABCA1 p.G1818E variant, the CETP variants p.Q337X, p.L290P, p.D459G and the splice-site variant c.1321 + 1G > A, the LCAT p.M276K variant, and the synonymous SCARB1 variant c.591C > T (p.G197G). In addition, population-level data from the UK Biobank were used to assess average HDL-C levels in variant carriers compared with non-carriers, supporting the functional interpretation and classification of variants (Table 1).

Variants found in both extreme ends of the lipid profile spectrum are less likely to be the primary genetic cause of the phenotype, thus eleven variants were classified as benign (class 1). Furthermore, seven variants were classified as likely benign (class 2), resulting in a total of 18 variants (47%) classified as not causative for the extreme HDL-C phenotype. This classification is in addition based on the high allele frequencies of these variants in the general population, in many cases their low evolutionary conservation across species, and evidence of normal protein activity in functional assays (S2–S6 Figs). Across all six genes, a total of 14 variants (37%) were assessed as variants of uncertain significance (class 3), lacking sufficient data to establish pathogenic potential. Noteworthy, although the number of variants found in ABCA1 and CETP exceeds the total found in the other four genes, the low frequency of class 3 variants in ABCA1 (1 of 12) and CETP (3 of 11) is a result of three recent studies on functional variant assessment [3638].

Only six variants were classified as likely pathogenic (class 4, n = 2) or pathogenic (class 5, n = 4). However, four additional variants of uncertain significance (class 3) showed evidence from functional assays and data from the UK Biobank suggesting that they may contribute to the HDL-C phenotype.

Variants contributing to abnormal HDL-C levels

Among individuals with HDL-C ≤ 0.5 mmol/L, we identified three pathogenic missense variants in five occurrences across four individuals: ABCA1 p.G1818E (n = 2), LCAT p.M276K (n = 2) and APOA1 p.R184L (n = 1), including one individual harboring both ABCA1 p.G1818E and LCAT p.M276K. While the APOA1 p.R184L and LCAT p.M276K have previously been associated with HDL deficiency [39,40], the ABCA1 p.G1818E variant represents a novel finding. Carriers of ABCA1 p.G1818E in the UK Biobank (n = 4) had in average a 32.75% lower HDL-C level compared to non-carriers. This variant also demonstrated only 31% of wild-type cholesterol efflux activity in functional assays (S2 Fig). Together, these findings provide sufficient evidence to classify the variant as likely pathogenic (class 4).

In the high HDL-C group, we identified three CETP variants with strong evidence for pathogenicity in six individuals: p.Q337X (n = 4), p.D459G (n = 1) and c.1321 + 1G > A (n = 1) (S3 Fig). Although the p.Q337X variant was reported in only one individual with reduced HDL-C compared to non-carriers in the UK Biobank data, all three variants were classified as class 5 (pathogenic) according to the ACMG guidelines.

Additionally, we identified four variants of uncertain significance that may contribute to elevated HDL-C levels. These include three CETP variants (p.D131N, p.L290P and p.E443K) and one synonymous variant in SCARB1 (c.591C > T; p.G197G) predicted to disrupt splicing. The CETP variants p.D131N, p.L290P, and p.E443K had multiple carriers in the UK Biobank and were associated with notable increases in HDL-C compared to non-carriers – 11.43%, 20.72%, and 25.27%, respectively, in addition to reduced protein functionality (S3 Fig). The SCARB1 p.G197G was not present in the UK Biobank data but induced an out-of-frame deletion of 41 nucleotides in exon 4 of SCARB1 (r.590_630del) when analyzed by minigene assay (S5 Fig). In coherence with the SpliceAI-predicted donor gain, this results in a premature stop codon early in SCARB1 exon 6, indicative of nonsense mediated decay degradation of the affected allele. The functional analyses of all four variants combined with elevated average HDL-C levels in carriers from the UK Biobank for the CETP variants support their potential pathogenicity.

Likely genetic causes were identified in 4 of 12 individuals (33.3%) in the low HDL-C group and in 10 of 198 individuals (5.05%) in the high HDL-C group (Table 2), in accordance with Sadananda et al. (35.9% in low HDL-C, 5.2% in high HDL-C) [35]. The average HDL-C level among individuals with likely pathogenic or pathogenic variants in the low HDL-C group was 0.53 mmol/L, slightly lower than the overall group average of 0.57 mmol/L. In the high HDL-C group, the corresponding average was 2.96 mmol/L, slightly higher than the group average of 2.87 mmol/L. Notably, when considering only the six individuals with variants classified as pathogenic (class 5), the average HDL-C level exceeded the study inclusion criteria, at 3.08 mmol/L. For clinical context, S4 Table summarizes variants previously identified at our diagnostic unit that are considered likely causes of abnormal HDL-C levels.

Table 2. Individuals with potentially causative variants of extreme HDL-C levels.

Individual Variant (Gene) Sex Age group HDL-C
Tromsø 4
(1994-1995)
Tromsø 5
(2001)
Tromsø 6
(2007-2008)
Tromsø 7
(2015-2016)
Low HDL-C
 1 R184L (APOA1) Male 50–59 0.36
 4 G1818E (ABCA1) Male 30–39 0.54 0.40
 6 G1818E (ABCA1)/M276K (LCAT) Male 50–59 0.63 0.47
 10 M276K (LCAT) Male 20–29 0.48 0.70 0.68
High HDL-C
 28 D131N (CETP) Male 50–59 1.73 1.97 3.30 2.80
 100 E443K (CETP) Female 30–39 2.66 3.10
 102 Q337X (CETP) Female 30–39 2.04 3.20 3.40
 110 Q337X (CETP) Male 60–69 2.77 2.66 3.30
 141 L290P (CETP) Female 50–59 3.16 3.00
 142 Q337X (CETP) Female 40–49 2.35 3.10 3.80
 166 c.1321 + 1G > A (CETP) Female 60–69 2.80 3.60
 192 c.591C > T (SCARB1) Female 40–49 3.40
 194 Q337X (CETP) Female 40–49 3.40
 200 D459G (CETP) Female 50 - 59 3.60

Four out of 12 individuals (33.33%) in the low HDL-C group (HDL-C ≤ 0.5 mmol/L) and 10 out of 198 individuals (5.05%) in the high HDL-C group (HDL-C ≥ 3.0 mmol/L) had genetic variants which could potentially explain their extreme HDL-C levels. The table displays an anonymous individual code, the identified variant along with the corresponding gene, sex and age group of the participants at first entry, and HDL-cholesterol (HDL-C) levels across the Tromsø Studies.

Discussion

Historical perspective and rationale for studying extreme HDL-C phenotypes

Individuals with extremely abnormal lipid levels are significantly more likely to carry rare, monogenic variants than those with values closer to the population mean [41,42]. Genetic testing of HDL-related dyslipidemia has thus primarily been reserved for individuals with HDL-C values at the extreme ends of the distribution. In our laboratory, these thresholds were defined as ≤ 0.5 mmol/L or ≥ 3.0 mmol/L – values that are exceptionally rare in the general population [39]. Since 2007, approximately 270 individuals have been tested – most referred due to a personal or family history of cardiovascular disease or dyslipidemia in combination with markedly abnormal HDL-C levels. To date, the unit has identified 41 likely genetic causes (25 variants) of abnormal HDL-C levels (S4 Table), corresponding to 15.19% of all referred individuals.

Given the growing body of evidence that both very low and very high HDL-C levels may be associated with increased overall mortality, the low frequency of HDL-related referrals to our clinic and the relatively high hit rate of pathogenic variants identified, we aimed to evaluate the prevalence of pathogenic variants in individuals with extreme HDL-C levels in a population-based setting. Specifically, we assessed some of the most prominent HDL-associated genes – ABCA1, APOA1, CETP, LCAT, PLTP and SCARB1. Through collaboration with the Tromsø Study, we identified 210 individuals eligible for genetic testing by the current HDL-C criteria from a cohort of 36 626 participants.

Genetic variants associated with abnormal HDL-C levels in study participants

Among the 210 individuals with abnormal HDL-C levels, 14 carried variants likely to explain their HDL-C phenotypes. Six of these variants were classified as pathogenic or likely pathogenic according to ACMG criteria, including LCAT p.M276K, APOA1 p.R184L and CETP p.Q337X, p.D459G and c.1321 + 1G > A. Additionally, the ABCA1 p.G1818E variant was classified as likely pathogenic when incorporating functional characterization from this study.

Several variants of uncertain significance appear to be strong candidates for pathogenicity based on in vitro functional data and population-level associations. The three CETP variants p.D131N, p.L290P and p.E443K all demonstrate reduced CETP function in vitro. Of these, p.L290P and p.E443K retained only 3% and 18% of wild-type CETP activity, respectively. Both variants have been identified in patients at our clinic with relatively high HDL-C: p.E443K in a male with HDL-C > 3 mmol/L and p.L290P in a female with HDL-C > 2.5 mmol/L. Support for their pathogenicity is strengthened by UK Biobank data, where carriers of p.E443K (n = 18) show an average HDL-C increase of 25.27% compared to non-carriers, while p.L290P showed even greater functional impairment which is supported by data from 182 carriers with an average HDL-C increase of 20.72%. Notably, p.E443K is one moderate ACMG criterion short of being reclassified as likely pathogenic (class 4). Although p.L290P currently fulfills fewer ACMG criteria than p.E443K, its combined functional and population-level data strongly support a causal role in elevated HDL-C levels.

The variant for which we have the least confidence, yet still consider potentially contributory, is CETP p.D131N. Functional assays indicated that this variant retains 64% of wild-type activity, suggesting a moderate reduction in function. However, UK Biobank data show that 61 carriers of p.D131N have an average HDL-C increase of 11.43%, exceeding the 7.75% increase observed in carriers of the pathogenic variant p.D459G (n = 158). Taken together, these findings support p.E443K and p.L290P as likely contributors to elevated HDL-C, while suggesting that p.D131N may exert a more modest but clinically relevant effect.

Koenig et al. recently identified the first reported SCARB1 null variant c.754_755delinsC together with p.G319V in compound heterozygote siblings with early-onset severe coronary artery disease [43]. The c.754_755delinsC variant introduces a frameshift-induced premature stop codon at p.253, resulting in minimal RNA and no detectable protein expression. The SCARB1 p.G197G variant identified in one Tromsø Study participant activates an alternative splice donor in exon 4, leading to a frameshift deletion and a premature stop codon at p.243. Although p.G197G does not meet ACMG criteria for likely pathogenicity, functional data reported by Koenig et al. indicate that a truncation at p.243 is also consistent with a SCARB1 null variant. Notably, both heterozygote and compound heterozygote cases in Koenig et al. had HDL-C levels within the normal range, underscoring a role for SR-B1 in severe atherosclerotic disease beyond extreme HDL-C levels.

Establishing new HDL-C thresholds for genetic testing: balancing prevalence, risk and yield

Despite extensive experience with genetic testing for elevated LDL-C at our diagnostic unit, amounting to nearly 70 000 individuals, testing for HDL-related disorders has historically remained limited. Several factors may contribute to this: the small number of known pathogenic variants, the perception that monogenic HDL disorders are exceedingly rare, limited clinical awareness, and variability in guideline recommendations. In addition, HDL-C has traditionally been regarded as the “good cholesterol”, primarily due to its inverse epidemiological association with CVD risk.

In recent years, this interpretation has been challenged. Observational studies have repeatedly demonstrated a U-shaped association between HDL-C and all-cause mortality, indicating that both very low and very high HDL-C levels are associated with increased risk. Madsen et al. showed that men with HDL-C ≥ 3.0 mmol/L had a twofold higher risk of all-cause mortality, while women with HDL-C ≥ 3.5 mmol/L had a 68% increased risk. Likewise, HDL-C < 1.0 mmol/L was associated with substantially higher mortality in both sexes. Moreover, Mendelian randomization studies and randomized trials have shown that altering HDL-C concentration itself does not reduce cardiovascular events, suggesting that HDL-C is more a biomarker of metabolic status than a direct causal factor for CVD [44]. Therapeutic strategies targeting CETP, ApoA1, ABCA1 and LCAT have increased HDL-C levels but have not led to improved cardiovascular outcomes [4547].

HDL-related genetic disorders also have implications extending beyond lipid metabolism and CVD. Variants in ABCA1 and CETP have been linked to Alzheimer’s disease, and APOA1 variants to amyloidosis [4850]. While monogenic causes of extreme HDL-C levels are rare, the prevalence and clinical impact of more common polygenic variation remain poorly understood. However, recent work using polygenic trait scores has shown that an excess burden of common HDL-associated variants can account for a substantial proportion of individuals with extreme HDL-C levels in referral cohorts [51]. As interest in HDL biology has renewed, accurate and equitable criteria for identifying individuals who may benefit from genetic testing have become increasingly important.

Clinical eligibility for HDL-related genetic testing has been based on strict, sex-neutral HDL-C thresholds (≤ 0.5 mmol/L or ≥ 3.0 mmol/L) at our diagnostic unit. In this study, such uniform cutoffs resulted in pronounced sex imbalance, with very low HDL-C occurring almost exclusively in men and very high HDL-C predominantly in women. This reflects well-established sex differences in HDL-C distribution and indicates that the previous criteria systematically biased access to genetic testing.

Population distribution data further showed that these thresholds were overly restrictive, identifying only a small fraction of individuals with extreme HDL-C (S1 Fig). Among women, approximately 0.15% had HDL-C ≥ 3.0 mmol/L, with a diagnostic yield of likely pathogenic variants comparable to that observed in other genetic testing contexts (4.88%) [5254], supporting retention of this upper threshold. Applying a similar tail-based approach across sexes yielded revised thresholds of ≤ 0.6 mmol/L or ≥ 2.7 mmol/L for men and ≤ 0.7 mmol/L or ≥ 3.0 mmol/L for women. These sex-specific limits better reflect population distributions, reduce bias in testing eligibility, and provide a pragmatic balance between diagnostic yield and resource use, although further validation in independent cohorts is warranted.

Variability of HDL-C levels and the importance of longitudinal data in genetic testing

Among the 210 individuals who met our inclusion criteria, most had data from multiple time points: 71 participated in two Tromsø surveys, 57 in three, and 37 in all four. When we examined the longitudinal data, we found that consistent extreme HDL-C levels were rare. In the low HDL-C group, only one individual maintained an average HDL-C level of ≤ 0.5 mmol/L across two surveys. Similarly, in the high HDL-C group, only 49 participants had a mean level of HDL-C ≥ 3.0 mmol/L or above (S1 Table).

HDL-C levels also varied over time in the participants with confirmed pathogenic variants. Each of the four individuals with low HDL-C had only one measurement ≤ 0.5 mmol/L. Even with the revised thresholds (HDL-C ≤ 0.6 mmol/L for men, HDL-C ≤ 0.7 mmol/L for women), two of the eight measurements of the four individuals would still exclude them for genetic testing. A similar pattern was observed in the high HDL-C group.

These findings highlight the substantial range of HDL-C levels in individuals with confirmed pathogenic variants, as well as the considerable intra-individual variability in HDL-C over time. Although our study lacks evidence of increased diagnostic yield, the new revised thresholds captured more individuals with pathogenic variants in both groups, when assessing the longitudinal average HDL-C levels. This underscores the importance of repeated measurements when evaluating extreme lipid phenotypes. Individuals with consistently low or high HDL-C levels – regardless of whether they fall within the established thresholds – should thus still be considered for genetic testing of HDL-related genes.

Limitations of study

The complex and dynamic nature of lipid metabolism complicates genotype–phenotype correlations in dyslipidemia. A key limitation of this study is therefore the restricted gene set analyzed, reflecting historical constraints of targeted genetic testing and limited DNA availability. Consequently, several HDL-associated genes beyond the canonical monogenic causes were not assessed.

Recent advances in clinical genetics now allow a more comprehensive approach. At our diagnostic unit, individuals with abnormal HDL-C are currently analyzed using whole genome sequencing (WGS) and a PanelApp-based gene panel with strong evidence of disease causation, including LPL, ANGPTL3, and LIPA [55]. Such an approach enables broader assessment of both monogenic and polygenic contributions to HDL metabolism and captures regulatory and non-coding variation [5660]. Nevertheless, even consensus gene panels do not encompass all genes implicated in HDL remodeling and clearance. In particular, LIPG and LIPC are not included in the gene panel and were not included in the present study, despite evidence linking rare variants in these genes to extreme HDL-C phenotypes [61,62]. Their exclusion therefore represents an additional limitation and underscores the need for continued refinement of genetic testing strategies for HDL-related dyslipidemia.

Elevated triglycerides and low HDL-C are hallmark features of metabolic syndrome, familial combined hyperlipidemia, and insulin resistance [6365]. These mechanisms suggest that individuals with both high triglycerides and low HDL-C are more likely to have secondary dyslipidemia rather than a primary genetic defect in HDL-related genes, emphasizing the importance of excluding secondary causes, before considering genetic testing for HDL disorders. Without the triglyceride data from the Tromsø Study, we cannot rule out metabolic syndrome as the cause of low HDL-C in the eight participants for whom no genetic cause was identified. Finally, we lacked systematic information on secondary causes of elevated HDL-C (e.g., alcohol intake, medications, hormonal therapy or liver disease), and cannot exclude that such factors contributed to the extreme HDL-C levels observed in some participants.

Conclusions

Genetic testing for HDL-related dyslipidemia is underutilized, with many individuals not meeting the current extreme HDL-C thresholds. Whereas monogenic HDL disorders are rare, our study identified several pathogenic variants in individuals with extreme HDL-C levels, where functional characterization, in combination with variant-specific phenotype data from the UK Biobank, substantially aided the pathogenicity assessment. Based on our findings, we propose revised sex-specific thresholds for genetic testing: HDL-C ≤ 0.6 mmol/L or ≥ 2.7 mmol/L for men, and HDL-C ≤ 0.7 mmol/L or ≥ 3.0 mmol/L for women. These adjusted thresholds are designed to alleviate sex discrimination while keeping testing volumes manageable. As our understanding of HDL-related genetic disorders evolves, further refinement of these thresholds and the integration of functional assays will enhance the identification and management of dyslipidemia, with ongoing research playing a pivotal role in shaping future diagnostic practices.

Supporting information

S1 File. Supplementary material and methods.

(PDF)

pone.0344627.s001.pdf (218.8KB, pdf)
S1 Table. An overview of all the individuals included in this study.

All individuals are indicated with sex, age group at first entry, lipid values (mmol/L) at the Tromsø 4 (1994–1995), 5 (2001), 6 (2007–2008) and 7 (2015–2016) studies and the mean HDL-cholesterol values.

(PDF)

pone.0344627.s002.pdf (407.8KB, pdf)
S2 Table. All missense variants in HDL-related genes in participants from the Tromsø Study.

Missense variants in ABCA1 (NM_005502.4), APOA1 (NM_000039.3), CETP (NM_000078.3), LCAT (NM_000229.2), PLTP (NM_006227.4) and SCARB1 (NM_005505.5) are annotated with respect to their effects at protein and nucleotide level. The reported lipid associated phenotypic effects of the variants, as well as the classifications made by Human Gene Mutation Database (HGMD) for variants reported in that database are shown. Also shown is an in silico prediction of pathogenicity represented by a REVEL score [66]. Allele frequencies of the variants are obtained from the Genome Aggregation Database (gnomAD, v.4.1.0). Pathogenicity classes of the variants were assessed according to the guidelines from The American College of Medical Genetics and Genomics and The Association for Molecular Pathology (ACMG), and the criteria used are indicated [21]. The number and percentage of variant carriers among the Tromsø study participants with high or low HDL-C are also indicated. HDL-C: HDL-cholesterol level. aHGMD HDL-related phenotype associated with the individual variant. bHGMD class: DM: Disease-causing mutation; DM?: Disease-causing mutation?; DP: Disease-associated polymorphism; FP: in vivo or in vitro functional polymorphism; DFP: Disease-associated polymorphism with supporting functional evidence; -: Not listed in HGMD. cA higher REVEL score (from 0 to 1) indicates a greater likelihood of a deleterious variant. dThe highest allele frequency among the populations: African/African American (AFR), Amish (AMI), Admixed American (AMR), Ashkenazi Jewish (ASJ), East Asian (EAS), Finnish (FIN), Middle Eastern (MID), Non-Finnish European (NFE) and South Asian (SAS) is shown. eClass 1: benign; Class 2: likely benign; Class 3: Unknown significance; Class 4: likely pathogenic; Class 5: pathogenic. fCriteria for pathogenicity weighed as strong (PS4, PM3_str, PP4_str), moderate (PS3_mod, PM2) or supporting (PS3–4_sup, PP3) and criteria for benignity weighed as stand-alone (BA1), strong (BS1–2), moderate (BS3_mod) or supporting (BP4).

(PDF)

pone.0344627.s003.pdf (171.8KB, pdf)
S3 Table. All silent or intronic variants in HDL-related genes in participants from the Tromsø Study.

Variants are annotated with respect to their effects at the protein and nucleotide level. The reported lipid associated phenotypic effects of the variants, as well as the classifications made by the Human Gene Mutation Database (HGMD) are shown. Also indicated are allele frequencies of the variants obtained from the Genome Aggregation Database (gnomAD, v4.1.0). Pathogenicity classes of the variants were assessed according to the guidelines from The American College of Medical Genetics and Genomics and The Association for Molecular Pathology (ACMG), and the criteria used are indicated [21]. The number and percentage of variant carriers among the Tromsø Study participants with high or low HDL-C are also indicated. HDL-C: HDL-cholesterol level. aHGMD reported phenotype associated with the individual variant. bHGMD class: DM: Disease-causing mutation; DM?: Disease-causing mutation?; DP: Disease-associated polymorphism; FP: in vivo or in vitro functional polymorphism; DFP: Disease-associated polymorphism with supporting functional evidence; -: Not listed in HGMD. cThe highest allele frequency among the populations: African/African American (AFR), Amish (AMI), Admixed American (AMR), Ashkenazi Jewish (ASJ), East Asian (EAS), Finnish (FIN), Middle Eastern (MID), Non-Finnish European (NFE) and South Asian (SAS) is shown. dClass 1: benign; Class 2: likely benign; Class 3: Unknown significance; Class 4: likely pathogenic; Class 5: pathogenic. eCriteria for pathogenicity weighed as strong (PS4, PM3_str, PP4_str), moderate (PS3_mod, PM2) or supporting (PS3_sup, PP3–4) and criteria for benignity weighed as stand alone (BA1), strong (BS1–2), moderate (BS3_mod) or supporting (BP4, BP7). fSpliceAI reports Δ scores ranging from 0 to 1 reporting the probability of splice alteration induced by the variant [67].

(PDF)

pone.0344627.s004.pdf (195KB, pdf)
S4 Table. Genetic variants found at our unit which are likely causes of abnormal HDL-C levels.

At the Unit for Cardiac and Cardiovascular Genetics, Oslo University Hospital, we have identified 25 likely causative genetic variants in 41 of 270 individuals which have been genetically tested for abnormal HDL-C levels. The indicated HDL-C levels (mmol/L) of individuals harboring the variants are shown, along with variant pathogenicity classes and the criteria applied according to the ACMG guidelines [21]. HDL-C: HDL-cholesterol. aClass 1: benign; Class 2: likely benign; Class 3: Unknown significance; Class 4: likely pathogenic; Class 5: pathogenic. bCriteria for pathogenicity weighed as very strong (PVS1), strong (PS4, PM3_str, PP4_str), moderate (PS3_mod, PM2–3) or supporting (PS3_sup, PM3–5_sup, PP3).

(PDF)

pone.0344627.s005.pdf (239.7KB, pdf)
S1 Fig. The distribution of HDL-C.

Two histograms depicting the distribution of HDL-cholesterol (HDL-C) levels in men and women. The data were provided by the Lipid Clinic in Norway, which obtained the information from Fürst Medical Laboratory, Oslo. The dataset pertains to individuals aged 18–49.9 years, primarily measured in general practice, and therefore, the sample is not representative of the general population. A table is included to display the number and percentage of individuals with HDL-C levels above or below specific thresholds.

(PDF)

pone.0344627.s006.pdf (201.3KB, pdf)
S2 Fig. Phenotype and functional assay of variants in ABCA1.

Selected ABCA1 missense variants found in the extreme ends of the HDL-C distribution in the Tromsø study were chosen for functional characterization. A) Participant HDL-C levels are given individually (female: light green; male: dark green) and as mean and standard deviation (SD) for each variant. B) Relative cholesterol efflux activity of ABCA1 missense variants (light blue) normalized to wild-type (WT, dark blue) in transiently transfected HEK293 cells. Two loss-of-function controls (white) are shown [36]. p values and effect size (g) compared to WT are given. One representative western blot showing protein amounts in lysates from transiently transfected HEK293 cells is shown.

(PDF)

pone.0344627.s007.pdf (205.9KB, pdf)
S3 Fig. Phenotype and functional assay of variants in CETP.

Selected CETP variants found in the extreme ends of the HDL-C distribution in the Tromsø study were chosen for functional characterization. *APRQ: p.A390P and p.R468Q. A) Participant HDL-C levels are given individually (female: light green; male: dark green) and as mean (SD) for each variant. B) Relative lipid transfer activity of CETP missense variants (light blue) normalized to wild-type (WT, dark blue) in media from transiently transfected HEK293 cells. One loss-of-function control (white) is shown [38]. p values and effect size (g) compared to WT are given. One representative western blot showing protein amounts in media and lysates from transiently transfected HEK293 cells is displayed. C) A DNA fragment spanning intron 13 to intron 15 in CETP was cloned into the pET01 minigene to characterize the consequence of the variant CETP c.1321 + 1G > A. Gel electrophoresis of RT-PCR outcome from transiently transfected HEK293 cells, in silico prediction from SpliceAI and sequencing result (consequence) are shown. Canonical exons are shown as boxes (pET01: white; CETP: blue) separated by introns (black horizontal lines). Solid black lines depict normal splicing (WT), disease-associated splicing indicated by dotted lines. Red arrow indicates the approximate location of the variant.

(PDF)

pone.0344627.s008.pdf (241.4KB, pdf)
S4 Fig. Phenotype and functional assay of variants in LCAT.

Selected LCAT missense variants found in the extreme ends of the HDL-C distribution in the Tromsø study were chosen for functional characterization. A) Participant HDL-C levels are given individually (female: light green; male: dark green) and as mean (SD) for each variant. B) Relative acyltransferase activity of LCAT missense variants (light blue) normalized to wild-type (WT, dark blue) in media from transiently transfected HEK293 cells. One loss-of-function control (white) is shown [68]. p values and effect size (g) compared to WT are given. One representative western blot showing protein amounts in media and lysates from transiently transfected HEK293 cells is shown.

(PDF)

pone.0344627.s009.pdf (189.9KB, pdf)
S5 Fig. Phenotype and functional assay of variants in SCARB1.

Selected SCARB1 variants found in the extreme ends of the HDL-C distribution in the Tromsø study were chosen for functional characterization. A) Participant HDL-C levels are given individually (female: light green; male: dark green) and as mean (SD) for each variant. B) Relative HDL-binding and uptake for SCARB1 missense variants (light blue) normalized to wild-type (WT, dark blue) in transiently transfected HEK293 cells. One loss-of-function control (white) is shown [69]. p values and effect size (g) compared to WT are given. One representative western blot showing protein amounts in media and lysates from transiently transfected HEK293 cells is displayed. C) A DNA fragment spanning intron 3 to intron 4 in SCARB1 was cloned into the pET01 minigene to characterize the consequence of the variant SCARB1 c.591C > T (p.G197G). Gel electrophoresis of RT-PCR outcome from transiently transfected HEK293 cells, in silico prediction from SpliceAI and sequencing result (consequence) are shown. Canonical exons are shown as boxes (pET01: white; SCARB1: blue) separated by introns (black horizontal lines). Solid black lines depict normal splicing (WT), disease-associated splicing indicated by dotted lines. Red arrow indicates the approximate location of the variant.

(PDF)

pone.0344627.s010.pdf (261.1KB, pdf)
S6 Fig. mRNA expression.

RNA was isolated from HEK293 cells transiently transfected with ABCA1, CETP, LCAT or SCARB1 wild-type (WT, dark blue columns), missense variants (light blue columns) and negative control variants (white columns). RNA was transcribed to cDNA, which was analyzed using PrimeTime Predesigned qPCR Assay primers. mRNA amounts were determined and normalized to the housekeeping gene GAPDH by the 2−ΔΔCt method [70] and normalized to WT in three independent experiments. Error bars represent 1 SD. *APRQ: p.A390P and p.R468Q.

(PDF)

pone.0344627.s011.pdf (203KB, pdf)
S1 Raw Images. Raw blot and gel images.

(PDF)

pone.0344627.s012.pdf (430.9KB, pdf)
S1 Raw Data. Raw data.

(PDF)

pone.0344627.s013.pdf (271.7KB, pdf)

Acknowledgments

We thank the Norwegian Health Association for their interest and engagement in this research. We would also like to thank the Tromsø Study for granting access to data and DNA samples from the 210 individuals with extreme HDL-C levels. Our appreciation extends to Kjetil Retterstøl and the Lipid Clinic in Norway, as well as to Fürst Medical Laboratory and its director, Håvard Selby Ebbestad, for providing the HDL-C distribution data. The present research has been conducted using the UK Biobank resource under application number 49823. We are most grateful to the Bioinformatics Core Facility of Nantes BiRD, member of Biogenouest, Institut Français de Bioinformatique (IFB) (ANR-11-INBS-0013) for the use of its resources and for its technical support.

Data Availability

All relevant data are within the paper and its Supporting information file.

Funding Statement

This research was supported by Nasjonalforeningen for Folkehelsen (Norwegian Health Association) (https://nasjonalforeningen.no/) (Grant No. 22741, received by K.B.). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

References

  • 1.Wilson PW, Abbott RD, Castelli WP. High density lipoprotein cholesterol and mortality. Arteriosclerosis. 1988;8(6):737–41. [DOI] [PubMed] [Google Scholar]
  • 2.Chang B, Laffin LJ, Sarraju A, Nissen SE. Obicetrapib-the rebirth of CETP inhibitors?. Curr Atheroscler Rep. 2024;26:603–8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Kaur N, Pandey A, Negi H, Shafiq N, Reddy S, Kaur H, et al. Effect of HDL-raising drugs on cardiovascular outcomes: a systematic review and meta-regression. PLoS One. 2014;9(4):e94585. doi: 10.1371/journal.pone.0094585 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Keene D, Price C, Shun-Shin MJ, Francis DP. Effect on cardiovascular risk of high density lipoprotein targeted drug treatments niacin, fibrates, and CETP inhibitors: meta-analysis of randomised controlled trials including 117,411 patients. BMJ. 2014;349:g4379. doi: 10.1136/bmj.g4379 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Lincoff AM, Nicholls SJ, Riesmeyer JS, Barter PJ, Brewer HB, Fox KAA, et al. Evacetrapib and Cardiovascular Outcomes in High-Risk Vascular Disease. N Engl J Med. 2017;376(20):1933–42. doi: 10.1056/NEJMoa1609581 [DOI] [PubMed] [Google Scholar]
  • 6.Hu W, Feng H, Liu Y, Xu X, Zhou P, Sun Z, et al. Recent advances in immunotherapy targeting CETP proteins for atherosclerosis prevention. Hum Vaccin Immunother. 2025;21(1):2462466. doi: 10.1080/21645515.2025.2462466 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.HPS3/TIMI55–REVEAL Collaborative Group, Bowman L, Hopewell JC, Chen F, Wallendszus K, Stevens W, et al. Effects of Anacetrapib in Patients with Atherosclerotic Vascular Disease. N Engl J Med. 2017;377(13):1217–27. doi: 10.1056/NEJMoa1706444 [DOI] [PubMed] [Google Scholar]
  • 8.Ko DT, Alter DA, Guo H, Koh M, Lau G, Austin PC, et al. High-Density Lipoprotein Cholesterol and Cause-Specific Mortality in Individuals Without Previous Cardiovascular Conditions: The CANHEART Study. J Am Coll Cardiol. 2016;68(19):2073–83. [DOI] [PubMed] [Google Scholar]
  • 9.Madsen CM, Varbo A, Nordestgaard BG. Extreme high high-density lipoprotein cholesterol is paradoxically associated with high mortality in men and women: two prospective cohort studies. Eur Heart J. 2017;38(32):2478–86. doi: 10.1093/eurheartj/ehx163 [DOI] [PubMed] [Google Scholar]
  • 10.Casula M, Colpani O, Xie S, Catapano AL, Baragetti A. HDL in Atherosclerotic Cardiovascular Disease: In Search of a Role. Cells. 2021;10(8):1869. doi: 10.3390/cells10081869 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Trimarco V, Izzo R, Morisco C, Mone P, Virginia Manzi M, Falco A, et al. High HDL (High-Density Lipoprotein) Cholesterol Increases Cardiovascular Risk in Hypertensive Patients. Hypertension. 2022;79(10):2355–63. doi: 10.1161/HYPERTENSIONAHA.122.19912 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Oram JF, Vaughan AM. ABCA1-mediated transport of cellular cholesterol and phospholipids to HDL apolipoproteins. Curr Opin Lipidol. 2000;11(3):253–60. doi: 10.1097/00041433-200006000-00005 [DOI] [PubMed] [Google Scholar]
  • 13.Fielding CJ, Fielding PE. Molecular physiology of reverse cholesterol transport. J Lipid Res. 1995;36(2):211–28. doi: 10.1016/s0022-2275(20)39898-9 [DOI] [PubMed] [Google Scholar]
  • 14.Tall AR. Plasma cholesteryl ester transfer protein. J Lipid Res. 1993;34(8):1255–74. doi: 10.1016/s0022-2275(20)36957-1 [DOI] [PubMed] [Google Scholar]
  • 15.Huuskonen J, Olkkonen VM, Jauhiainen M, Ehnholm C. The impact of phospholipid transfer protein (PLTP) on HDL metabolism. Atherosclerosis. 2001;155(2):269–81. doi: 10.1016/s0021-9150(01)00447-6 [DOI] [PubMed] [Google Scholar]
  • 16.Zannis VI, Fotakis P, Koukos G, Kardassis D, Ehnholm C, Jauhiainen M, et al. HDL biogenesis, remodeling, and catabolism. Handb Exp Pharmacol. 2015;224:53–111. doi: 10.1007/978-3-319-09665-0_2 [DOI] [PubMed] [Google Scholar]
  • 17.Linton MF, Yancey PG, Tao H, Davies SS. HDL Function and Atherosclerosis: Reactive Dicarbonyls as Promising Targets of Therapy. Circ Res. 2023;132(11):1521–45. doi: 10.1161/CIRCRESAHA.123.321563 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.Hovingh GK, de Groot E, van der Steeg W, Boekholdt SM, Hutten BA, Kuivenhoven JA, et al. Inherited disorders of HDL metabolism and atherosclerosis. Curr Opin Lipidol. 2005;16(2):139–45. doi: 10.1097/01.mol.0000162318.47172.ef [DOI] [PubMed] [Google Scholar]
  • 19.Brunham LR, Hegele RA. What is the prevalence of familial hypercholesterolemia? Arterioscler Thromb Vasc Biol. 2021;41(10):2629–31. [DOI] [PubMed] [Google Scholar]
  • 20.Dong W, Wong KHY, Liu Y, Levy-Sakin M, Hung W-C, Li M, et al. Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia. J Lipid Res. 2022;63(6):100209. doi: 10.1016/j.jlr.2022.100209 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–24. doi: 10.1038/gim.2015.30 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Walker LC, de la Hoya M, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, et al. Application of the ACMG/AMP framework to capture evidence relevant to predicted and observed impact on splicing: recommendations from the ClinGen SVI splicing subgroup. medRxiv. 2023. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Eggen AE, Mathiesen EB, Wilsgaard T, Jacobsen BK, Njølstad I. The sixth survey of the Tromso Study (Tromso 6) in 2007-08: collaborative research in the interface between clinical medicine and epidemiology: study objectives, design, data collection procedures, and attendance in a multipurpose population-based health survey. Scand J Public Health. 2013;41(1):65–80. doi: 10.1177/1403494812469851 [DOI] [PubMed] [Google Scholar]
  • 24.Maruyama T, Sakai N, Ishigami M, Hirano K, Arai T, Okada S, et al. Prevalence and phenotypic spectrum of cholesteryl ester transfer protein gene mutations in Japanese hyperalphalipoproteinemia. Atherosclerosis. 2003;166(1):177–85. doi: 10.1016/s0021-9150(02)00327-1 [DOI] [PubMed] [Google Scholar]
  • 25.Zanoni P, Khetarpal SA, Larach DB, Hancock-Cerutti WF, Millar JS, Cuchel M, et al. Rare variant in scavenger receptor BI raises HDL cholesterol and increases risk of coronary heart disease. Science. 2016;351(6278):1166–71. doi: 10.1126/science.aad3517 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Geller AS, Polisecki EY, Diffenderfer MR, Asztalos BF, Karathanasis SK, Hegele RA, et al. Genetic and secondary causes of severe HDL deficiency and cardiovascular disease. J Lipid Res. 2018;59(12):2421–35. doi: 10.1194/jlr.M088203 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Sudlow C, Gallacher J, Allen N, Beral V, Burton P, Danesh J, et al. UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med. 2015;12(3):e1001779. doi: 10.1371/journal.pmed.1001779 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Van Hout CV, Tachmazidou I, Backman JD, Hoffman JD, Liu D, Pandey AK, et al. Exome sequencing and characterization of 49,960 individuals in the UK Biobank. Nature. 2020;586(7831):749–56. doi: 10.1038/s41586-020-2853-0 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10(2):giab008. doi: 10.1093/gigascience/giab008 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Lindenbaum P, Redon R. bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files. Bioinformatics. 2018;34(7):1224–5. doi: 10.1093/bioinformatics/btx734 [DOI] [PubMed] [Google Scholar]
  • 31.Harrison SM, Biesecker LG, Rehm HL. Overview of Specifications to the ACMG/AMP Variant Interpretation Guidelines. Curr Protoc Hum Genet. 2019;103(1):e93. doi: 10.1002/cphg.93 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 32.Chora JR, Iacocca MA, Tichý L, Wand H, Kurtz CL, Zimmermann H, et al. The Clinical Genome Resource (ClinGen) Familial Hypercholesterolemia Variant Curation Expert Panel consensus guidelines for LDLR variant classification. Genet Med. 2022;24(2):293–306. doi: 10.1016/j.gim.2021.09.012 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Yokoyama S. Unique features of high-density lipoproteins in the Japanese: in population and in genetic factors. Nutrients. 2015;7(4):2359–81. doi: 10.3390/nu7042359 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Mogadam M, Ahmed SW, Mensch AH, Godwin ID. Within-person fluctuations of serum cholesterol and lipoproteins. Arch Intern Med. 1990;150(8):1645–8. doi: 10.1001/archinte.1990.00040031645011 [DOI] [PubMed] [Google Scholar]
  • 35.Sadananda SN, Foo JN, Toh MT, Cermakova L, Trigueros-Motos L, Chan T, et al. Targeted next-generation sequencing to diagnose disorders of HDL cholesterol. J Lipid Res. 2015;56(10):1993–2001. doi: 10.1194/jlr.P058891 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 36.Teigen M, Ølnes ÅS, Bjune K, Leren TP, Bogsrud MP, Strøm TB. Functional characterization of missense variants affecting the extracellular domains of ABCA1 using a fluorescence-based assay. J Lipid Res. 2024;65(1):100482. doi: 10.1016/j.jlr.2023.100482 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 37.Teigen M, Ølnes ÅS, Bjune K, Bogsrud MP, Strøm TB. Functional characterization of genetic variants affecting the intracellular domains of ATP-binding cassette transporter A1 (ABCA1). J Lipid Res. 2025;66(8):100854. doi: 10.1016/j.jlr.2025.100854 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 38.Ølnes ÅS, Teigen M, Laerdahl JK, Leren TP, Strøm TB, Bjune K. Variants in the CETP gene affect levels of HDL cholesterol by reducing the amount, and not the specific lipid transfer activity, of secreted CETP. PLoS One. 2023;18(12):e0294764. doi: 10.1371/journal.pone.0294764 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Berge KE, Leren TP. Mutations in APOA-I and ABCA1 in Norwegians with low levels of HDL cholesterol. Clin Chim Acta. 2010;411(23–24):2019–23. doi: 10.1016/j.cca.2010.08.027 [DOI] [PubMed] [Google Scholar]
  • 40.Skretting G, Blomhoff JP, Solheim J, Prydz H. The genetic defect of the original Norwegian lecithin:cholesterol acyltransferase deficiency families. FEBS Lett. 1992;309(3):307–10. doi: 10.1016/0014-5793(92)80795-i [DOI] [PubMed] [Google Scholar]
  • 41.Hegele RA. Plasma lipoproteins: genetic influences and clinical implications. Nat Rev Genet. 2009;10(2):109–21. doi: 10.1038/nrg2481 [DOI] [PubMed] [Google Scholar]
  • 42.Lee EY, Yang Y, Kim HS, Cho JH, Yoon KH, Chung WS, et al. Effect of visit-to-visit LDL-, HDL-, and non-HDL-cholesterol variability on mortality and cardiovascular outcomes after percutaneous coronary intervention. Atherosclerosis. 2018;279:1–9. [DOI] [PubMed] [Google Scholar]
  • 43.Koenig SN, Sucharski HC, Jose EM, Dudley EK, Madiai F, Cavus O, et al. Inherited Variants in SCARB1 Cause Severe Early-Onset Coronary Artery Disease. Circ Res. 2021;129(2):296–307. doi: 10.1161/CIRCRESAHA.120.318793 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 44.Kjeldsen EW, Thomassen JQ, Frikke-Schmidt R. HDL cholesterol concentrations and risk of atherosclerotic cardiovascular disease - Insights from randomized clinical trials and human genetics. Biochim Biophys Acta Mol Cell Biol Lipids. 2022;1867(1):159063. doi: 10.1016/j.bbalip.2021.159063 [DOI] [PubMed] [Google Scholar]
  • 45.Nicholls SJ, Nelson AJ, Ditmarsch M, Kastelein JJP, Ballantyne CM, Ray KK, et al. Safety and Efficacy of Obicetrapib in Patients at High Cardiovascular Risk. N Engl J Med. 2025;393(1):51–61. doi: 10.1056/NEJMoa2415820 [DOI] [PubMed] [Google Scholar]
  • 46.Lan NSR, Watts GF. Quo vadis after AEGIS: new opportunities for therapies targeted at reverse cholesterol transport?. Curr Atheroscler Rep. 2025;27(1):35. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 47.Verbrugge FH, Krychtiuk KA. In perspective: CSL112 (apolipoprotein A-I) infusions and cardiovascular outcomes in patients with acute myocardial infarction: the ApoA-I Event Reducing in Ischemic Syndromes II (AEGIS-II) trial. Eur Heart J Acute Cardiovasc Care. 2024;13(4):362–4. doi: 10.1093/ehjacc/zuae046 [DOI] [PubMed] [Google Scholar]
  • 48.Lewandowski CT, Laham MS, Thatcher GRJ. Remembering your A, B, C’s: Alzheimer’s disease and ABCA1. Acta Pharm Sin B. 2022;12(3):995–1018. doi: 10.1016/j.apsb.2022.01.011 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 49.Poliakova T, Wellington CL. Roles of peripheral lipoproteins and cholesteryl ester transfer protein in the vascular contributions to cognitive impairment and dementia. Mol Neurodegener. 2023;18(1):86. doi: 10.1186/s13024-023-00671-y [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 50.Ioannou A, Porcari A, Patel RK, Razvi Y, Sinigiani G, Martinez-Naharro A, et al. Rare Forms of Cardiac Amyloidosis: Diagnostic Clues and Phenotype in Apo AI and AIV Amyloidosis. Circ Cardiovasc Imaging. 2023;16(7):523–35. doi: 10.1161/CIRCIMAGING.123.015259 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 51.Dron JS, Wang J, Low-Kam C, Khetarpal SA, Robinson JF, McIntyre AD, et al. Polygenic determinants in extremes of high-density lipoprotein cholesterol. J Lipid Res. 2017;58(11):2162–70. doi: 10.1194/jlr.M079822 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 52.Stava TT, Leren TP, Bogsrud MP. Molecular genetics in 4408 cardiomyopathy probands and 3008 relatives in Norway: 17 years of genetic testing in a national laboratory. Eur J Prev Cardiol. 2022;29(13):1789–99. doi: 10.1093/eurjpc/zwac102 [DOI] [PubMed] [Google Scholar]
  • 53.Stava TT, Berge KE, Haugaa KH, Smedsrud MK, Leren TP, Bogsrud MP. Molecular genetics in 1991 arrhythmia probands and 2782 relatives in Norway: Results from 17 years of genetic testing in a national laboratory. Clin Genet. 2024;106(5):585–602. doi: 10.1111/cge.14593 [DOI] [PubMed] [Google Scholar]
  • 54.Leren TP, Bogsrud MP. Cascade screening for familial hypercholesterolemia should be organized at a national level. Curr Opin Lipidol. 2022;33(4):231–6. doi: 10.1097/MOL.0000000000000832 [DOI] [PubMed] [Google Scholar]
  • 55.Martin AR, Williams E, Foulger RE, Leigh S, Daugherty LC, Niblock O, et al. PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels. Nat Genet. 2019;51(11):1560–5. doi: 10.1038/s41588-019-0528-2 [DOI] [PubMed] [Google Scholar]
  • 56.Brousseau ME, Goldkamp AL, Collins D, Demissie S, Connolly AC, Cupples LA, et al. Polymorphisms in the gene encoding lipoprotein lipase in men with low HDL-C and coronary heart disease: the Veterans Affairs HDL Intervention Trial. J Lipid Res. 2004;45(10):1885–91. doi: 10.1194/jlr.M400152-JLR200 [DOI] [PubMed] [Google Scholar]
  • 57.Jin W, Marchadier D, Rader DJ. Lipases and HDL metabolism. Trends Endocrinol Metab. 2002;13(4):174–8. doi: 10.1016/s1043-2760(02)00589-1 [DOI] [PubMed] [Google Scholar]
  • 58.Aghasizadeh M, Ahmadi Hoseini A, Sahebi R, Kazemi T, Asadiyan-Sohan P, Esmaily H, et al. Association of a genetic variant in angiopoietin-like 3 with serum HDL-C and risk of cardiovascular disease: A study of the MASHAD cohort over 6 years. Mol Genet Genomic Med. 2024;12(4):e2418. doi: 10.1002/mgg3.2418 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 59.Bowden KL, Bilbey NJ, Bilawchuk LM, Boadu E, Sidhu R, Ory DS, et al. Lysosomal acid lipase deficiency impairs regulation of ABCA1 gene and formation of high density lipoproteins in cholesteryl ester storage disease. J Biol Chem. 2011;286(35):30624–35. doi: 10.1074/jbc.M111.274381 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 60.Motazacker MM, Peter J, Treskes M, Shoulders CC, Kuivenhoven JA, Hovingh GK. Evidence of a polygenic origin of extreme high-density lipoprotein cholesterol levels. Arterioscler Thromb Vasc Biol. 2013;33(7):1521–8. doi: 10.1161/ATVBAHA.113.301505 [DOI] [PubMed] [Google Scholar]
  • 61.Edmondson AC, Brown RJ, Kathiresan S, Cupples LA, Demissie S, Manning AK, et al. Loss-of-function variants in endothelial lipase are a cause of elevated HDL cholesterol in humans. J Clin Invest. 2009;119(4):1042–50. doi: 10.1172/JCI37176 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 62.Pirim D, Bunker CH, Hokanson JE, Hamman RF, Demirci FY, Kamboh MI. Hepatic lipase (LIPC) sequencing in individuals with extremely high and low high-density lipoprotein cholesterol levels. PLoS One. 2020;15(12):e0243919. doi: 10.1371/journal.pone.0243919 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 63.Ginsberg HN, Zhang Y-L, Hernandez-Ono A. Metabolic syndrome: focus on dyslipidemia. Obesity (Silver Spring). 2006;14 Suppl 1:41S-49S. doi: 10.1038/oby.2006.281 [DOI] [PubMed] [Google Scholar]
  • 64.Welty FK. How do elevated triglycerides and low HDL-cholesterol affect inflammation and atherothrombosis?. Curr Cardiol Rep. 2013;15(9):400. doi: 10.1007/s11886-013-0400-4 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 65.Filtz A, Parihar S, Greenberg GS, Park CM, Scotti A, Lorenzatti D, et al. New approaches to triglyceride reduction: Is there any hope left?. Am J Prev Cardiol. 2024;18:100648. doi: 10.1016/j.ajpc.2024.100648 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 66.Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, et al. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. Am J Hum Genet. 2016;99(4):877–85. doi: 10.1016/j.ajhg.2016.08.016 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 67.de Sainte Agathe J-M, Filser M, Isidor B, Besnard T, Gueguen P, Perrin A, et al. SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation. Hum Genomics. 2023;17(1):7. doi: 10.1186/s40246-023-00451-1 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 68.Fotakis P, Kuivenhoven JA, Dafnis E, Kardassis D, Zannis VI. The Effect of Natural LCAT Mutations on the Biogenesis of HDL. Biochemistry. 2015;54(21):3348–59. doi: 10.1021/acs.biochem.5b00180 [DOI] [PubMed] [Google Scholar]
  • 69.May SC, Dron JS, Hegele RA, Sahoo D. Human variant of scavenger receptor BI (R174C) exhibits impaired cholesterol transport functions. J Lipid Res. 2021;62:100045. doi: 10.1016/j.jlr.2021.100045 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 70.Livak KJ, Schmittgen TD. Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method. Methods. 2001;25(4):402–8. doi: 10.1006/meth.2001.1262 [DOI] [PubMed] [Google Scholar]

Decision Letter 0

Chiara Pavanello

13 Jan 2026

Dear Dr. Ølnes,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Feb 27 2026 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

  • A letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols....

We look forward to receiving your revised manuscript.

Kind regards,

Chiara Pavanello

Academic Editor

PLOS One

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1.Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and

https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf

2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match.

When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section.

3. Thank you for stating the following in the Acknowledgments Section of your manuscript:

“We would like to express our gratitude to the Norwegian Health Association for their financial support 484 of this study. We also thank the Tromsø Study for granting access to data and DNA samples from the 485 210 individuals with extreme HDL-C levels. Our appreciation extends to Kjetil Retterstøl and the Lipid 486 Clinic in Norway, as well as to Fürst Medical Laboratory and its director, Håvard Selby Ebbestad, for 487 providing the HDL-C distribution data. The present research has been conducted using the UK Biobank 488 resource under application number 49823. We are most grateful to the Bioinformatics Core Facility of 489 Nantes BiRD, member of Biogenouest, Institut Français de Bioinformatique (IFB) (ANR-11-INBS490 0013) for the use of its resources and for its technical support.”

We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form.

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

“This research was supported by the Norwegian Health Association (https://nasjonalforeningen.no/) (Grant No. 22741 received by K.B.). The funding body had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.”

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

4. We note that there is identifying data in the Supporting Information file  “S1_Table.pdf” Due to the inclusion of these potentially identifying data, we have removed this file from your file inventory. Prior to sharing human research participant data, authors should consult with an ethics committee to ensure data are shared in accordance with participant consent and all applicable local laws.

Data sharing should never compromise participant privacy. It is therefore not appropriate to publicly share personally identifiable data on human research participants. The following are examples of data that should not be shared:

-Name, initials, physical address

-Ages more specific than whole numbers

-Internet protocol (IP) address

-Specific dates (birth dates, death dates, examination dates, etc.)

-Contact information such as phone number or email address

-Location data

-ID numbers that seem specific (long numbers, include initials, titled “Hospital ID”) rather than random (small numbers in numerical order)

Data that are not directly identifying may also be inappropriate to share, as in combination they can become identifying. For example, data collected from a small group of participants, vulnerable populations, or private groups should not be shared if they involve indirect identifiers (such as sex, ethnicity, location, etc.) that may risk the identification of study participants.

Additional guidance on preparing raw data for publication can be found in our Data Policy (https://journals.plos.org/plosone/s/data-availability#loc-human-research-participant-data-and-other-sensitive-data) and in the following article: http://www.bmj.com/content/340/bmj.c181.long.

Please remove or anonymize all personal information (<specific identifying information in file to be removed>), ensure that the data shared are in accordance with participant consent, and re-upload a fully anonymized data set. Please note that spreadsheet columns with personal information must be removed and not hidden as all hidden columns will appear in the published file.

5. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data.

6. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well.

7. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

8. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

[Note: HTML markup is below. Please do not edit.]

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #1: Yes

Reviewer #2: Yes

**********

2. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.-->

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: Yes

Reviewer #2: Yes

**********

Reviewer #1: Ølnes et al. investigated the genetic basis of extreme HDL-C levels in a population-based cohort in Northern Norway, using data from the Tromsø Study. This is a well-conducted and clearly presented study that investigates an underexplored area of lipid genetic: HDL-related dyslipidemia. The integration of functional assays and UK Biobank data strengthens the interpretation of the identified variants. The statistical analyses conducted are appropriate for the study design and objectives. Overall, the manuscript is well written and structured.

Minor comments:

- In some cases, the term “HDL” is used instead of “HDL-C” to describe HDL concentration. For clarity, consider using “HDL-C” when referring to measured concentrations

- On page 4, the authors state “In Norway, patients with extreme HDL-C levels have been offered genetic testing of the five key genes”, whereas in this study six genes are analyzed. Please clarify the reason for this difference

- On page 4, the authors report that approximately 270 individuals with extreme HDL-C levels and more than 70,000 individuals with abnormal LDL-C levels have been genetically analyzed in Norway over the past 25 years. Please clarify if the reported numbers are based on previously published data or reflect the authors’ own clinical experience

- Page 19, line 373: for consistency with the rest of the manuscript, consider replacing the term “mutations” with “variants”, and formatting the gene symbols according to standard gene nomenclature

Reviewer #2: This study aims to assess the prevalence of genetic variants responsible for extremely low and high levels of HDL-C using longitudinal data from the Tromsø Study, a population-based cohort in Northern Norway. In 210 individuals with extreme HDL-C levels, 38 variants of interest across six HDL-related genes were identified, of which 10 were considered potentially causative, found in 14 individuals. Sex-specific analyses showed that using HDL-C thresholds aligned with population distributions improved detection of individuals with pathogenic variants. These findings are clinically important in the context of raising awareness of the deleterious associations of extreme HDL-C with cardiovascular disease. The data are sound and the manuscript is well-written. However, the authors still need to address a short list of concerns as listed below.

Major points

1. Methods: The definitions of extremely low and high HDL-C levels appear arbitrary and should be supported by relevant references.

2. Results: The description of the supplementary data (Figures S1 to S6) in the text of the manuscript is unsatisfactory. These data should be presented in more details. Figure S6 should be described in the Results section, not in the Discussion.

Minor points

1. Introduction and throughout the manuscript: The terms “HDL levels” and HDL-C levels” seem to be used as synonyms, which is not always appropriate (e.g. lines 76-77). Please revise.

2. Results: Table S4 contains important data on the pathogenicity of genetic variants and should be moved to the main manuscript.

3. Discussion, p. 21: LPL directly contributes to the circulating HDL pool by producing surface remnants of triglyceride-rich lipoproteins rich in phospholipids and free cholesterol. Please revise.

4. The Discussion section is too lengthy and should be shortened.

**********

what does this mean?). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our Privacy Policy..-->

Reviewer #1: No

Reviewer #2: No

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures

You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation.

NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications.

PLoS One. 2026 Apr 20;21(4):e0344627. doi: 10.1371/journal.pone.0344627.r002

Author response to Decision Letter 1


4 Feb 2026

Response to comments from the reviewers on Manuscript Number: PONE-D-25-62448

Response to Reviewer #1

We thank Reviewer #1 for the thorough and positive evaluation of our manuscript, and for the constructive comments. We are pleased that the reviewer finds the study well conducted, clearly presented, and strengthened by the integration of functional assays and UK Biobank data. Below, we address each comment in detail.

Minor comments

1. “In some cases, the term ‘HDL’ is used instead of ‘HDL-C’ to describe HDL concentration. For clarity, consider using ‘HDL-C’ when referring to measured concentrations.”

Response:

We agree and thank the reviewer for pointing this out. The manuscript has been carefully revised to ensure consistent use of “HDL-C” whenever referring to measured cholesterol concentrations, while “HDL” is reserved for particle/function-related descriptions. These changes have been implemented throughout the text.

2. “On page 4, the authors state that patients with extreme HDL-C levels have been offered genetic testing of five key genes, whereas six genes are analyzed in this study. Please clarify the reason for this difference.”

Response:

Thank you for highlighting this important point. We have now clarified this explicitly in the Introduction.

Briefly, PLTP is not part of the routine diagnostic gene panel for HDL-related dyslipidemia at our unit. However, in the context of this study, we had sufficient DNA material to sequence one additional gene beyond the standard panel. We therefore chose to include PLTP for two main reasons:

1. We anticipated that PLTP variants could be assessed using the same experimental system as CETP variants (although this later proved not to be feasible for functional assays), and

2. PLTP is relatively understudied in the context of extreme HDL-C phenotypes, and we aimed to explore its potential contribution and variant frequency in a population-based setting.

This rationale has now been clearly stated in the revised manuscript (Introduction), to avoid confusion between routine diagnostics and the research-based gene selection in this study.

3. “Please clarify if the reported numbers are based on previously published data or reflect the authors’ own clinical experience.”

Response:

We have now added an explicit statement in the revised manuscript clarifying that these numbers do not represent previously published data, but instead reflect diagnostic activity at our clinical genetic unit.

Specifically, the figures refer to patients referred for and analyzed by genetic testing at the Unit for Cardiac and Cardiovascular Genetics, Oslo University Hospital, over the past 25 years. This additional clarification has been included in the Introduction to ensure transparency regarding the data source.

4. “For consistency, consider replacing the term ‘mutations’ with ‘variants’, and formatting gene symbols according to standard gene nomenclature.”

Response:

We agree with this comment. The manuscript has been revised accordingly:

The term “mutations” has been replaced with “variants” throughout the text, and all gene symbols are now consistently formatted according to standard gene nomenclature.

Once again, we thank Reviewer #1 for the careful reading of our manuscript and for the constructive suggestions, which have helped improve clarity and precision.

Response to Reviewer #2

We thank Reviewer #2 for the careful reading of our manuscript and for the positive assessment of the data quality, clinical relevance, and clarity of the presentation. We particularly appreciate the recognition of the clinical importance of raising awareness of the deleterious associations of extreme HDL-C levels with cardiovascular disease. Below, we address each of the reviewer’s concerns in detail.

Major points

1. “The definitions of extremely low and high HDL-C levels appear arbitrary and should be supported by relevant references.”

Response:

We thank the reviewer for raising this point. We agree that, without adequate explanation, the HDL-C thresholds used in this study (≤ 0.5 mmol/L and ≥ 3.0 mmol/L) may indeed appear arbitrary, and we acknowledge that this was not sufficiently clear in the original version of the manuscript.

These thresholds were not derived from population-based percentiles, but were historically defined by clinicians at our diagnostic unit more than a decade ago, within a markedly different clinical and scientific landscape. At that time, genetic testing was resource-intensive and costly, laboratory capacity was limited, and clinical awareness of HDL-related disorders was low. Healthcare systems, including the Norwegian public healthcare system, emphasized cost–benefit considerations, avoidance of unnecessary testing, and prioritization of limited genetic resources toward conditions with established therapeutic consequences. Together, these factors favored the use of particularly strict eligibility criteria for genetic testing.

Importantly, these stringent thresholds were selected in clinical settings to enrich for individuals with a high likelihood of monogenic causes of extreme HDL-C levels. We have now added references supporting the biological relevance of the applied cutoffs and reflecting the evidence base that informed the original diagnostic criteria.

Since then, the clinical and scientific landscape has changed substantially. There is now increased recognition of the association between extreme HDL-C levels and adverse outcomes, greater interest in HDL biology, and markedly reduced costs and increased capacity for genetic testing.

We fully agree with the reviewer that these historical thresholds were unusually strict. Importantly, recognizing this limitation is a central motivation for the present study. By leveraging population-based data, we demonstrate that the previous cutoffs introduced a pronounced sex bias and captured only a small fraction of individuals with potentially pathogenic variants. In response, and partly informed by the work conducted during the preparation of this manuscript, the criteria for clinical genetic testing at our unit have now been revised toward less extreme, sex-specific thresholds. The Methods and Discussion sections have been revised to more clearly explain the origin of the original cutoffs, their limitations, the clinical reasoning underlying the updated thresholds, and the references used.

2. “The description of the supplementary data (Figures S1 to S6) in the text of the manuscript is unsatisfactory. These data should be presented in more detail. Figure S6 should be described in the Results section, not in the Discussion.”

Response:

The supplementary figures are now described in greater detail in the Results section, with explicit references to the relevant figures. And to improve logical flow and clarity, the supplementary figures have been renumbered: the former S6 Fig is now S1 Fig, and the previous S1–S5 Figs are now S2–S6 Figs.

Minor points

1. “The terms ‘HDL levels’ and ‘HDL-C levels’ seem to be used as synonyms.”

Response:

We agree with this comment. The manuscript has been revised to ensure consistent and appropriate use of terminology: “HDL-C” is now used when referring to measured cholesterol concentrations, whereas “HDL” is reserved for particle- or function-related contexts.

2. “Table S4 contains important data on the pathogenicity of genetic variants and should be moved to the main manuscript.”

Response:

We appreciate the reviewer’s suggestion and understand the rationale for highlighting these data. Table S4 summarizes genetic variants previously identified at our diagnostic unit and is intended to provide additional clinical context based on our cumulative experience with HDL-related disorders. These variants are independent of the Tromsø Study cohort and do not originate from the population-based material analyzed in the present study.

For this reason, we chose to place Table S4 in the supplementary material, in order to clearly distinguish historical diagnostic findings from the primary results derived from the Tromsø Study. We felt that including these data in the main manuscript might risk blurring this distinction.

That said, we acknowledge the reviewer’s point that the information may be of interest to readers. If the reviewer or editor considers it important to move Table S4 to the main manuscript, we would of course be happy to do so or to revise its presentation accordingly.

3. “LPL directly contributes to the circulating HDL pool by producing surface remnants of triglyceride-rich lipoproteins rich in phospholipids and free cholesterol. Please revise.”

Response:

Thank you for this clarification. When shortening the Discussion section (Minor comment #4), we decided to remove the description of the roles of each protein mentioned in “Limitations of the study” (ANGPTL3, LPL, LAL, hepatic and endothelial lipase). If the reviewer or editor finds it important to include these descriptions, we will include them in the manuscript and make sure that LPL’s role is correctly explained.

4. “The Discussion section is too lengthy and should be shortened.”

Response:

We agree and have substantially revised the Discussion section. The total length has been reduced from 2264 words to 1823 words, corresponding to an approximate 20% reduction, while preserving the key clinical, methodological, and interpretative points. Redundant passages have been removed or condensed, and the overall structure has been tightened to improve readability.

Once again, we thank Reviewer #2 for the thoughtful and constructive feedback, which has led to improvements in clarity, structure, and contextualization of the manuscript.

Response to Academic Editor

We thank the Academic Editor for the careful assessment of our manuscript and for the clear and constructive guidance, which has helped us improve the manuscript’s compliance with PLOS ONE’s policies and standards.

1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming.

Response:

We have carefully reviewed the manuscript and all associated files and ensured that they comply with PLOS ONE’s style and file-naming requirements.

2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match.

Response:

All funding-related text has been removed from the manuscript. The amended Funding Statement has been included in the revised cover letter, as requested.

3. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

“This research was supported by the Norwegian Health Association (https://nasjonalforeningen.no/) (Grant No. 22741 received by K.B.). The funding body had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.”

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

Response:

The amended statement has been included in the revised cover letter.

4. We note that there is identifying data in the Supporting Information file “S1_Table.pdf” Due to the inclusion of these potentially identifying data, we have removed this file from your file inventory. Prior to sharing human research participant data, authors should consult with an ethics committee to ensure data are shared in accordance with participant consent and all applicable local laws.

Data sharing should never compromise participant privacy. It is therefore not appropriate to publicly share personally identifiable data on human research participants.

Please remove or anonymize all personal information (<specific identifying information in file to be removed>), ensure that the data shared are in accordance with participant consent, and re-upload a fully anonymized data set. Please note that spreadsheet columns with personal information must be removed and not hidden as all hidden columns will appear in the published file.

Response:

We have revised S1 Table to further anonymize the data by replacing specific participant ages with age groups and have ensured that the data shared are in accordance with participant consent and applicable regulations. The updated, anonymized S1 Table has been re-uploaded to the file inventory. Corresponding changes have also been made in Table 2 in the main manuscript.

5. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data.

Response:

We have removed the phrase “data not shown” and the corresponding statement from the figure legend of S3 Fig, as the information was not essential to the presentation or interpretation of the results.

6. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well.

Response:

The ethics statement has been revised in the Methods section to explicitly state that written informed consent was obtained from all participants.

7. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise.

Response:

No specific recommendations to cite additional publications were made by the reviewers.

8. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Response:

The reference list has been carefully reviewed. No retracted articles are cited.

Additional changes:

In addition to the revisions described above, we have carefully reviewed and refined the pathogenicity interpretation of several genetic variants based on constructive feedback received from a member of a PhD defense committee, who had access to the manuscript through its inclusion in a doctoral dissertation. Corresponding updates have been made to Tables S2–S4. These refinements enhance the scientific rigor and clarity of the manuscript and do not alter the main findings or conclusions of the study.

Attachment

Submitted filename: Response to Reviewers.docx

pone.0344627.s015.docx (26KB, docx)

Decision Letter 1

Chiara Pavanello

23 Feb 2026

Genetic testing in individuals with extreme HDL-C levels: diagnostic yield and clinical implications from the Tromsø Study

PONE-D-25-62448R1

Dear Dr. Ølnes,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact  and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact  and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact  and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support....

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Chiara Pavanello

Academic Editor

PLOS One

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions??>

Reviewer #1: (No Response)

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #1: (No Response)

Reviewer #2: (No Response)

**********

4. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.-->

Reviewer #1: (No Response)

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: (No Response)

Reviewer #2: Yes

**********

Reviewer #1: (No Response)

Reviewer #2: All comments have been addressed. I have no further suggestions and thank the authors for their work.

**********

what does this mean?). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our For information about this choice, including consent withdrawal, please see our Privacy Policy..-->

Reviewer #1: No

Reviewer #2: No

**********

Acceptance letter

Chiara Pavanello

PONE-D-25-62448R1

PLOS One

Dear Dr. Ølnes,

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS One. Congratulations! Your manuscript is now being handed over to our production team.

At this stage, our production department will prepare your paper for publication. This includes ensuring the following:

* All references, tables, and figures are properly cited

* All relevant supporting information is included in the manuscript submission,

* There are no issues that prevent the paper from being properly typeset

You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps.

Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing.

If we can help with anything else, please email us at customercare@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Chiara Pavanello

Academic Editor

PLOS One

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 File. Supplementary material and methods.

    (PDF)

    pone.0344627.s001.pdf (218.8KB, pdf)
    S1 Table. An overview of all the individuals included in this study.

    All individuals are indicated with sex, age group at first entry, lipid values (mmol/L) at the Tromsø 4 (1994–1995), 5 (2001), 6 (2007–2008) and 7 (2015–2016) studies and the mean HDL-cholesterol values.

    (PDF)

    pone.0344627.s002.pdf (407.8KB, pdf)
    S2 Table. All missense variants in HDL-related genes in participants from the Tromsø Study.

    Missense variants in ABCA1 (NM_005502.4), APOA1 (NM_000039.3), CETP (NM_000078.3), LCAT (NM_000229.2), PLTP (NM_006227.4) and SCARB1 (NM_005505.5) are annotated with respect to their effects at protein and nucleotide level. The reported lipid associated phenotypic effects of the variants, as well as the classifications made by Human Gene Mutation Database (HGMD) for variants reported in that database are shown. Also shown is an in silico prediction of pathogenicity represented by a REVEL score [66]. Allele frequencies of the variants are obtained from the Genome Aggregation Database (gnomAD, v.4.1.0). Pathogenicity classes of the variants were assessed according to the guidelines from The American College of Medical Genetics and Genomics and The Association for Molecular Pathology (ACMG), and the criteria used are indicated [21]. The number and percentage of variant carriers among the Tromsø study participants with high or low HDL-C are also indicated. HDL-C: HDL-cholesterol level. aHGMD HDL-related phenotype associated with the individual variant. bHGMD class: DM: Disease-causing mutation; DM?: Disease-causing mutation?; DP: Disease-associated polymorphism; FP: in vivo or in vitro functional polymorphism; DFP: Disease-associated polymorphism with supporting functional evidence; -: Not listed in HGMD. cA higher REVEL score (from 0 to 1) indicates a greater likelihood of a deleterious variant. dThe highest allele frequency among the populations: African/African American (AFR), Amish (AMI), Admixed American (AMR), Ashkenazi Jewish (ASJ), East Asian (EAS), Finnish (FIN), Middle Eastern (MID), Non-Finnish European (NFE) and South Asian (SAS) is shown. eClass 1: benign; Class 2: likely benign; Class 3: Unknown significance; Class 4: likely pathogenic; Class 5: pathogenic. fCriteria for pathogenicity weighed as strong (PS4, PM3_str, PP4_str), moderate (PS3_mod, PM2) or supporting (PS3–4_sup, PP3) and criteria for benignity weighed as stand-alone (BA1), strong (BS1–2), moderate (BS3_mod) or supporting (BP4).

    (PDF)

    pone.0344627.s003.pdf (171.8KB, pdf)
    S3 Table. All silent or intronic variants in HDL-related genes in participants from the Tromsø Study.

    Variants are annotated with respect to their effects at the protein and nucleotide level. The reported lipid associated phenotypic effects of the variants, as well as the classifications made by the Human Gene Mutation Database (HGMD) are shown. Also indicated are allele frequencies of the variants obtained from the Genome Aggregation Database (gnomAD, v4.1.0). Pathogenicity classes of the variants were assessed according to the guidelines from The American College of Medical Genetics and Genomics and The Association for Molecular Pathology (ACMG), and the criteria used are indicated [21]. The number and percentage of variant carriers among the Tromsø Study participants with high or low HDL-C are also indicated. HDL-C: HDL-cholesterol level. aHGMD reported phenotype associated with the individual variant. bHGMD class: DM: Disease-causing mutation; DM?: Disease-causing mutation?; DP: Disease-associated polymorphism; FP: in vivo or in vitro functional polymorphism; DFP: Disease-associated polymorphism with supporting functional evidence; -: Not listed in HGMD. cThe highest allele frequency among the populations: African/African American (AFR), Amish (AMI), Admixed American (AMR), Ashkenazi Jewish (ASJ), East Asian (EAS), Finnish (FIN), Middle Eastern (MID), Non-Finnish European (NFE) and South Asian (SAS) is shown. dClass 1: benign; Class 2: likely benign; Class 3: Unknown significance; Class 4: likely pathogenic; Class 5: pathogenic. eCriteria for pathogenicity weighed as strong (PS4, PM3_str, PP4_str), moderate (PS3_mod, PM2) or supporting (PS3_sup, PP3–4) and criteria for benignity weighed as stand alone (BA1), strong (BS1–2), moderate (BS3_mod) or supporting (BP4, BP7). fSpliceAI reports Δ scores ranging from 0 to 1 reporting the probability of splice alteration induced by the variant [67].

    (PDF)

    pone.0344627.s004.pdf (195KB, pdf)
    S4 Table. Genetic variants found at our unit which are likely causes of abnormal HDL-C levels.

    At the Unit for Cardiac and Cardiovascular Genetics, Oslo University Hospital, we have identified 25 likely causative genetic variants in 41 of 270 individuals which have been genetically tested for abnormal HDL-C levels. The indicated HDL-C levels (mmol/L) of individuals harboring the variants are shown, along with variant pathogenicity classes and the criteria applied according to the ACMG guidelines [21]. HDL-C: HDL-cholesterol. aClass 1: benign; Class 2: likely benign; Class 3: Unknown significance; Class 4: likely pathogenic; Class 5: pathogenic. bCriteria for pathogenicity weighed as very strong (PVS1), strong (PS4, PM3_str, PP4_str), moderate (PS3_mod, PM2–3) or supporting (PS3_sup, PM3–5_sup, PP3).

    (PDF)

    pone.0344627.s005.pdf (239.7KB, pdf)
    S1 Fig. The distribution of HDL-C.

    Two histograms depicting the distribution of HDL-cholesterol (HDL-C) levels in men and women. The data were provided by the Lipid Clinic in Norway, which obtained the information from Fürst Medical Laboratory, Oslo. The dataset pertains to individuals aged 18–49.9 years, primarily measured in general practice, and therefore, the sample is not representative of the general population. A table is included to display the number and percentage of individuals with HDL-C levels above or below specific thresholds.

    (PDF)

    pone.0344627.s006.pdf (201.3KB, pdf)
    S2 Fig. Phenotype and functional assay of variants in ABCA1.

    Selected ABCA1 missense variants found in the extreme ends of the HDL-C distribution in the Tromsø study were chosen for functional characterization. A) Participant HDL-C levels are given individually (female: light green; male: dark green) and as mean and standard deviation (SD) for each variant. B) Relative cholesterol efflux activity of ABCA1 missense variants (light blue) normalized to wild-type (WT, dark blue) in transiently transfected HEK293 cells. Two loss-of-function controls (white) are shown [36]. p values and effect size (g) compared to WT are given. One representative western blot showing protein amounts in lysates from transiently transfected HEK293 cells is shown.

    (PDF)

    pone.0344627.s007.pdf (205.9KB, pdf)
    S3 Fig. Phenotype and functional assay of variants in CETP.

    Selected CETP variants found in the extreme ends of the HDL-C distribution in the Tromsø study were chosen for functional characterization. *APRQ: p.A390P and p.R468Q. A) Participant HDL-C levels are given individually (female: light green; male: dark green) and as mean (SD) for each variant. B) Relative lipid transfer activity of CETP missense variants (light blue) normalized to wild-type (WT, dark blue) in media from transiently transfected HEK293 cells. One loss-of-function control (white) is shown [38]. p values and effect size (g) compared to WT are given. One representative western blot showing protein amounts in media and lysates from transiently transfected HEK293 cells is displayed. C) A DNA fragment spanning intron 13 to intron 15 in CETP was cloned into the pET01 minigene to characterize the consequence of the variant CETP c.1321 + 1G > A. Gel electrophoresis of RT-PCR outcome from transiently transfected HEK293 cells, in silico prediction from SpliceAI and sequencing result (consequence) are shown. Canonical exons are shown as boxes (pET01: white; CETP: blue) separated by introns (black horizontal lines). Solid black lines depict normal splicing (WT), disease-associated splicing indicated by dotted lines. Red arrow indicates the approximate location of the variant.

    (PDF)

    pone.0344627.s008.pdf (241.4KB, pdf)
    S4 Fig. Phenotype and functional assay of variants in LCAT.

    Selected LCAT missense variants found in the extreme ends of the HDL-C distribution in the Tromsø study were chosen for functional characterization. A) Participant HDL-C levels are given individually (female: light green; male: dark green) and as mean (SD) for each variant. B) Relative acyltransferase activity of LCAT missense variants (light blue) normalized to wild-type (WT, dark blue) in media from transiently transfected HEK293 cells. One loss-of-function control (white) is shown [68]. p values and effect size (g) compared to WT are given. One representative western blot showing protein amounts in media and lysates from transiently transfected HEK293 cells is shown.

    (PDF)

    pone.0344627.s009.pdf (189.9KB, pdf)
    S5 Fig. Phenotype and functional assay of variants in SCARB1.

    Selected SCARB1 variants found in the extreme ends of the HDL-C distribution in the Tromsø study were chosen for functional characterization. A) Participant HDL-C levels are given individually (female: light green; male: dark green) and as mean (SD) for each variant. B) Relative HDL-binding and uptake for SCARB1 missense variants (light blue) normalized to wild-type (WT, dark blue) in transiently transfected HEK293 cells. One loss-of-function control (white) is shown [69]. p values and effect size (g) compared to WT are given. One representative western blot showing protein amounts in media and lysates from transiently transfected HEK293 cells is displayed. C) A DNA fragment spanning intron 3 to intron 4 in SCARB1 was cloned into the pET01 minigene to characterize the consequence of the variant SCARB1 c.591C > T (p.G197G). Gel electrophoresis of RT-PCR outcome from transiently transfected HEK293 cells, in silico prediction from SpliceAI and sequencing result (consequence) are shown. Canonical exons are shown as boxes (pET01: white; SCARB1: blue) separated by introns (black horizontal lines). Solid black lines depict normal splicing (WT), disease-associated splicing indicated by dotted lines. Red arrow indicates the approximate location of the variant.

    (PDF)

    pone.0344627.s010.pdf (261.1KB, pdf)
    S6 Fig. mRNA expression.

    RNA was isolated from HEK293 cells transiently transfected with ABCA1, CETP, LCAT or SCARB1 wild-type (WT, dark blue columns), missense variants (light blue columns) and negative control variants (white columns). RNA was transcribed to cDNA, which was analyzed using PrimeTime Predesigned qPCR Assay primers. mRNA amounts were determined and normalized to the housekeeping gene GAPDH by the 2−ΔΔCt method [70] and normalized to WT in three independent experiments. Error bars represent 1 SD. *APRQ: p.A390P and p.R468Q.

    (PDF)

    pone.0344627.s011.pdf (203KB, pdf)
    S1 Raw Images. Raw blot and gel images.

    (PDF)

    pone.0344627.s012.pdf (430.9KB, pdf)
    S1 Raw Data. Raw data.

    (PDF)

    pone.0344627.s013.pdf (271.7KB, pdf)
    Attachment

    Submitted filename: Response to Reviewers.docx

    pone.0344627.s015.docx (26KB, docx)

    Data Availability Statement

    All relevant data are within the paper and its Supporting information file.


    Articles from PLOS One are provided here courtesy of PLOS

    RESOURCES