PURPOSE: In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published consensus standardized guidelines for sequence-level variant classification in Mendelian disorders. To increase accuracy and consistency, the Clinical Genome Resource Familial Hypercholesterolemia (FH) Variant Curation Expert Panel was tasked with optimizing the existing ACMG/AMP framework for disease-specific classification in FH. In this study, we provide consensus recommendations for the most common FH-associated gene, LDLR, where >2300 unique FH-associated variants have been identified. METHODS: The multidisciplinary FH Variant Curation Expert Panel met in person and through frequent emails and conference calls to develop LDLR-specific modifications of ACMG/AMP guidelines. Through iteration, pilot testing, debate, and commentary, consensus among experts was reached. RESULTS: The consensus LDLR variant modifications to existing ACMG/AMP guidelines include (1) alteration of population frequency thresholds, (2) delineation of loss-of-function variant types, (3) functional study criteria specifications, (4) cosegregation criteria specifications, and (5) specific use and thresholds for in silico prediction tools, among others. CONCLUSION: Establishment of these guidelines as the new standard in the clinical laboratory setting will result in a more evidence-based, harmonized method for LDLR variant classification worldwide, thereby improving the care of patients with FH.

Academic Medical Center Erasmus University Rotterdam Netherlands

Ambry Genetics Aliso Viejo CA

Bristol Genetics Laboratory North Bristol NHS Trust Bristol United Kingdom

Centre for Cardiovascular Genetics Institute of Cardiovascular Science University College London London United Kingdom

Centre for Cardiovascular Surgery and Transplantation Brno Czech Republic; Faculty of Medicine Masaryk University Brno Czech Republic

Centre of Molecular Biology and Gene Therapy University Hospital Brno Brno Czech Republic

Color Health Inc Burlingame CA

Department of Clinical Biochemistry PathWest Laboratory Medicine WA Royal Perth Hospital and Fiona Stanley Hospital Network University of Western Australia Perth Western Australia Australia

Department of Genetics School of Medicine University of North Carolina at Chapel Hill Chapel Hill NC

Department of Health Promotion and Prevention of Noncommunicable Diseases Nacional Institute of Health Dr Ricardo Jorge Lisbon Portugal; BioISI BioSystems and Integrative Sciences Institute Department of Chemistry and Biochemistry Faculty of Sciences University of Lisbon Lisbon Portugal

Department of Medicine Faculty of Medicine The University of British Columbia Vancouver British Columbia Canada

Departments of Biomedical Data Science and Pathology School of Medicine Stanford University Stanford CA; Center for Inherited Cardiovascular Disease Stanford Health Care Stanford University Stanford CA

Departments of Biomedical Data Science and Pathology School of Medicine Stanford University Stanford CA; Department of Paediatric Laboratory Medicine The Hospital for Sick Children Toronto Ontario Canada

Division of Cardiovascular Medicine Stanford Cardiovascular Institute Prevention Research Center and Diabetes Research Center School of Medicine Stanford University Stanford CA; FH Foundation Pasadena CA

GeneDx Inc Gaithersburg MD

Genomics England London United Kingdom

Laboratory of Genetics and Molecular Cardiology Institute of the Hearth Faculty of Medicine São Paulo University São Paulo Brazil

Robarts Research Institute Schulich School of Medicine and Dentistry Western University London Ontario Canada

University Hospitals Pitié Salpêtrière Charles Foix Molecular and Chromosomal Genetics Center Obesity and Dyslipidemia Genetics Unit Sorbonne University Paris France

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Akioyamen LE, Genest J, Shan SD, et al. Estimating the prevalence of heterozygous familial hypercholesterolaemia: a systematic review and meta-analysis. BMJ Open. 2017;7(9):e016461. 10.1136/bmjopen-2017-016461. PubMed DOI PMC

Nordestgaard BG, Chapman MJ, Humphries SE, et al. Familial hypercholesterolaemia is underdiagnosed and undertreated in the general population: guidance for clinicians to prevent coronary heart disease: consensus statement of the European Atherosclerosis Society. Eur Heart J. 2013;34(45):3478–3490a. Published correction appears in Eur Heart J. 2020;41(47):4517. 10.1093/eurheartj/eht273. PubMed DOI PMC

Nordestgaard BG, Benn M. Genetic testing for familial hypercholesterolaemia is essential in individuals with high LDL cholesterol: who does it in the world? Eur Heart J. 2017;38(20):1580–1583. 10.1093/eurheartj/ehx136. PubMed DOI

Austin MA, Hutter CM, Zimmern RL, Humphries SE. Genetic causes of monogenic heterozygous familial hypercholesterolemia: a HuGE prevalence review. Am J Epidemiol. 2004;160(5):407–420. 10.1093/aje/kwh236. PubMed DOI

Cenarro A, Etxebarria A, De Castro-Orós I, et al. The p.Leu167del mutation in APOE gene causes autosomal dominant hypercholesterolemia by down-regulation of LDL receptor expression in hepatocytes. J Clin Endocrinol Metab. 2016;101(5):2113–2121. 10.1210/jc.2015-3874. PubMed DOI

NICE National Institute for Health and Care Excellence. Familial hypercholesterolaemia: identification and management. NICE National Institute for Health and Care Excellence. Published August 27, 2008. Updated October 04, 2019. https://www.nice.org.uk/guidance/CG71. Accessed November 2, 2020.

Sturm AC, Knowles JW, Gidding SS, et al. Clinical genetic testing for familial hypercholesterolemia: JACC scientific expert panel. J Am Coll Cardiol. 2018;72(6):662–680. 10.1016/j.jacc.2018.05.044. PubMed DOI

Khoury MJ, Bowen MS, Clyne M, et al. From public health genomics to precision public health: a 20-year journey. Genet Med. 2018;20(6):574–582. 10.1038/gim.2017.211. PubMed DOI PMC

Kalia SS, Adelman K, Bale SJ, et al. Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics. Genet Med. 2017;19(2):249–255. Published correction appears in Genet Med. 2017;19(4):484. 10.1038/gim.2016.190. PubMed DOI

Iacocca MA, Hegele RA. Recent advances in genetic testing for familial hypercholesterolemia. Expert Rev Mol Diagn. 2017;17(7):641–651. 10.1080/14737159.2017.1332997. PubMed DOI

Iacocca MA, Chora JR, Carrié A, et al. ClinVar database of global familial hypercholesterolemia-associated DNA variants. Hum Mutat. 2018;39(11):1631–1640. 10.1002/humu.23634. PubMed DOI PMC

Richards S, Aziz N, Bale S, 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):405–424. 10.1038/gim.2015.30. PubMed DOI PMC

Rehm HL, Berg JS, Brooks LD, et al. ClinGen—the clinical genome resource. N Engl J Med. 2015;372(23):2235–2242. 10.1056/NEJMsr1406261. PubMed DOI PMC

Chora JR, Medeiros AM, Alves AC, Bourbon M. Analysis of publicly available LDLR, APOB, and PCSK9 variants associated with familial hypercholesterolemia: application of ACMG guidelines and implications for familial hypercholesterolemia diagnosis. Genet Med. 2018;20(6):591–598. 10.1038/gim.2017.151. PubMed DOI

Whiffin N, Minikel E, Walsh R, et al. Using high-resolution variant frequencies to empower clinical genome interpretation. Genet Med. 2017;19(10):1151–1158. 10.1038/gim.2017.26. PubMed DOI PMC

Iacocca MA, Hegele RA. Role of DNA copy number variation in dyslipidemias. Curr Opin Lipidol. 2018;29(2):125–132. 10.1097/MOL.0000000000000483. PubMed DOI

Abou Tayoun AN, Pesaran T, DiStefano MT, et al. Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criteria. Hum Mutat. 2018;39(11):1517–1524. 10.1002/humu.23626. PubMed DOI PMC

Chen WJ, Goldstein JL, Brown MS. NPXY, a sequence often found in cytoplasmic tails, is required for coated pit-mediated internalization of the low density lipoprotein receptor. J Biol Chem. 1990;265(6):3116–3123. PubMed

Brnich SE, Abou Tayoun AN, Couch FJ, et al. Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. Genome Med. 2019;12(1):3. 10.1186/s13073-019-0690-2. PubMed DOI PMC

Wijers M, Kuivenhoven JA, van de Sluis B. The life cycle of the low-density lipoprotein receptor: insights from cellular and in-vivo studies. Curr Opin Lipidol. 2015;26(2):82–87. 10.1097/MOL.0000000000000157. PubMed DOI

Soutar AK, Naoumova RP. Mechanisms of disease: genetic causes of familial hypercholesterolemia. Nat Clin Pract Cardiovasc Med. 2007;4(4):214–225. 10.1038/ncpcardio0836. PubMed DOI

Brown MS, Goldstein JL. A receptor-mediated pathway for cholesterol homeostasis (Nobel lecture). Angew Chem Int Ed Engl. 1986;25(7):583–602. 10.1002/anie.198605833. DOI

Hobbs HH, Brown MS, Goldstein JL. Molecular genetics of the LDL receptor gene in familial hypercholesterolemia. Hum Mutat. 1992;1(6):445–466. 10.1002/humu.1380010602. PubMed DOI

Bourbon M, Alves AC, Sijbrands EJ. Low-density lipoprotein receptor mutational analysis in diagnosis of familial hypercholesterolemia. Curr Opin Lipidol. 2017;28(2):120–129. 10.1097/MOL.0000000000000404. PubMed DOI

Russell DW, Brown MS, Goldstein JL. Different combinations of cysteine-rich repeats mediate binding of low density lipoprotein receptor to two different proteins. J Biol Chem. 1989;264(36):21682–21688. PubMed

Jeon H, Blacklow SC. Structure and physiologic function of the low-density lipoprotein receptor. Annu Rev Biochem. 2005;74:535–562. 10.1146/annurev.biochem.74.082803.133354. PubMed DOI

Russell DW, Lehrman MA, Südhof TC, et al. The LDL receptor in familial hypercholesterolemia: use of human mutations to dissect a membrane protein. Cold Spring Harb Symp Quant Biol. 1986;51(Pt 2):811–819. 10.1101/sqb.1986.051.01.094. PubMed DOI

van der Graaf A, Avis HJ, Kusters DM, et al. Molecular basis of autosomal dominant hypercholesterolemia: assessment in a large cohort of hypercholesterolemic children. Circulation. 2011;123(11):1167–1173. 10.1161/CIRCULATIONAHA.110.979450. PubMed DOI

Starr B, Hadfield SG, Hutten BA, et al. Development of sensitive and specific age- and gender-specific low-density lipoprotein cholesterol cutoffs for diagnosis of first-degree relatives with familial hypercholesterolaemia in cascade testing. Clin Chem Lab Med. 2008;46(6):791–803. 10.1515/CCLM.2008.135. PubMed DOI

Defesche JC, Lansberg PJ, Umans-Eckenhausen MA, Kastelein JJ. Advanced method for the identification of patients with inherited hypercholesterolemia. Semin Vasc Med. 2004;4(1):59–65. 10.1055/s-2004-822987. PubMed DOI

Scientific Steering Committee on behalf of the Simon Broome Register Group. Risk of fatal coronary heart disease in familial hypercholesterolaemia. Scientific Steering Committee on behalf of the Simon Broome Register Group. BMJ. 1991;303(6807):893–896. 10.1136/bmj.303.6807.893. PubMed DOI PMC

Williams RR, Hunt SC, Schumacher MC, et al. Diagnosing heterozygous familial hypercholesterolemia using new practical criteria validated by molecular genetics. Am J Cardiol. 1993;72(2):171–176. 10.1016/0002-9149(93)90155-6. PubMed DOI

Ruel I, Aljenedil S, Sadri I, et al. Imputation of baseline LDL cholesterol concentration in patients with familial hypercholesterolemia on statins or ezetimibe. Clin Chem. 2018;64(2):355–362. 10.1373/clinchem.2017.279422. PubMed DOI

Baigent C, Keech A, Kearney PM, et al. Efficacy and safety of cholesterol-lowering treatment: prospective meta-analysis of data from 90,056 participants in 14 randomised trials of statins. Lancet. 2005;366(9493):1267–1278. Published correction appears in Lancet. 2005;366(9494):1358. Published correction appears in Lancet. 2008;371(9630):2084. 10.1016/S0140-6736(05)67394-1. PubMed DOI

Trinder M, Francis GA, Brunham LR. Association of monogenic vs polygenic hypercholesterolemia with risk of atherosclerotic cardiovascular disease. JAMA Cardiol. 2020;5(4):390–399. Published correction appears in JAMA Cardiol. 2020;5(4):488. 10.1001/jamacardio.2019.5954. PubMed DOI PMC

Emi M, Hegele RM, Hopkins PN, et al. Effects of three genetic loci in a pedigree with multiple lipoprotein phenotypes. Arterioscler Thromb. 1991;11(5):1349–1355. 10.1161/01.atv.11.5.1349. PubMed DOI

Motazacker MM, Pirruccello J, Huijgen R, et al. Advances in genetics show the need for extending screening strategies for autosomal dominant hypercholesterolaemia. Eur Heart J. 2012;33(11):1360–1366. 10.1093/eurheartj/ehs010. PubMed DOI

Ioannidis NM, Rothstein JH, Pejaver V, et al. REVEL: an ensemble method for predicting the pathogenicity of rare missense variants. Am J Hum Genet. 2016;99(4):877–885. 10.1016/j.ajhg.2016.08.016. PubMed DOI PMC

Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol. 2004;11(2-3):377–394. 10.1089/1066527041410418. PubMed DOI

Cassanelli S, Bertolini S, Rolleri M, et al. A ‘de novo’ point mutation of the low-density lipoprotein receptor gene in an Italian subject with primary hypercholesterolemia. Clin Genet. 1998;53(5):391–395. 10.1111/j.1399-0004.1998.tb02752.x. PubMed DOI

Thormaehlen A, Schuberth C, Won H-H, et al. Systematic cell-based phenotyping of missense alleles empowers rare variant association studies: a case for LDLR and myocardial infarction. PLoS Genet. 2015;11(2):e1004855. 10.1371/journal.pgen.1004855. PubMed DOI PMC

Weile J, Roth FP. Multiplexed assays of variant effects contribute to a growing genotype–phenotype atlas. Hum Genet. 2018;137:665–678. 10.1007/s00439-018-1916-x. PubMed DOI PMC

Functional characterization of 16 variants found in the LDL receptor gene

2023 Update on European Atherosclerosis Society Consensus Statement on Homozygous Familial Hypercholesterolaemia: new treatments and clinical guidance