Analysis of publicly available LDLR, APOB, and PCSK9 variants associated with familial hypercholesterolemia: application of ACMG guidelines and implications for familial hypercholesterolemia diagnosis

Abstract

PurposeFamilial hypercholesterolemia (FH) is an autosomal disorder of lipid metabolism presenting with increased cardiovascular risk. Although more than 1,700 variants have been associated with FH, the great majority have not been functionally proved to affect the low-density lipoprotein receptor cycle. We aimed to classify all described variants associated with FH and to establish the proportion of variants that lack evidence to support their pathogenicity.MethodsWe followed American College of Medical Genetics and Genomics (ACMG) guidelines for the classification, and collected information from a variety of databases and individual reports. A worldwide overview of publicly available FH variants was also performed.ResultsA total of 2,104 unique variants were identified as being associated with FH, but only 166 variants have been proven by complete in vitro functional studies to be causative of disease. Additionally, applying the ACMG guidelines, 1,097 variants were considered pathogenic or likely pathogenic. Only seven variants were found in all five continents.ConclusionThe lack of functional evidence for about 85% of all variants found in FH patients can compromise FH diagnosis and patient prognosis. ACMG classification improves variant interpretation, but functional studies are necessary to understand the effect of about 40% of all variants reported. Nevertheless, ACMG guidelines need to be adapted to FH for a better diagnosis.

The familial hypercholesterolaemia phenotype: Monogenic familial hypercholesterolaemia, polygenic hypercholesterolaemia and other causes

“…In the Portuguese FH Study only if a variant is classified as pathogenic or likely pathogenic (ACMG), or if the variant is designated as a VUS, only after functional in vitro assessment with proof of affected function, the clinician is informed that the variant found confirms or is consistent with the clinical diagnosis. Due to the establishment of functional studies in our lab, the majority of the mutations found in the Portuguese population (120/142) have a classification of pathogenic or likely pathogenic following ACMG guidelines, and this results in more than 80% of our cohort of FH/M+ patients having a molecularly confirmed FH diagnosis. The implementation of functional studies as an adjunct to work in diagnostic laboratories improves the genetic diagnosis of FH, and should be encouraged worldwide.…”

“…22 All variants were checked with Mutalyzer 2.0, as recommended by HGVS. Variants were classified as pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign or benign, according to the American College of Medical Genetics and Genomics (ACMG) guidelines 23 following specific adaptations described in Chora et al 24 The variants reported in the present study were considered novel if they were not described before in public databases 25,26 or in PUBMED, and novel for Portugal if they were found for the first time in Portugal, but have been previously reported in another country. In silico analysis was performed as described before.…”

Screening for familial hypercholesterolaemia in primary care: Time for general practice to play its part

“…NICE guidelines [17] also advocate that only relatives of genetically positive index cases should be offered genetic testing to establish mutation positive FH. The obvious downside is that with over 1700 known FH mutations [48], not all are amenable to genetic testing and up to 40% may be missed [9].…”

Ultrassequenciamento exômico dos principais genes relacionados com a hipercolesterolemia familial

“…As principais alterações no LDLR são as mutações na extremidade 5'UTR (0,8%), pequenas deleções (1,6%), grandes rearranjos cromossômicos (9,0%), mutações sem sentindo (nonsense, 9,0%), mutações por deslocamento (frameshift, 18,0%), mutações na região de processamento de RNA (splicing, 9,0%) e mutação de sentido trocado (missense, 46,0%) (CHORA et al, 2018;MARDUEL et al, 2010).…”

“…Avaliar a relação das diferentes variantes encontradas por ultrassequenciamento em pacientes com HF é de grande importância para compreender os mecanismos pelos quais as variações genéticas influenciam na concentração de colesterol e consequentemente o processo patológico desta doença (FORTI et al, 2003;SILVA et al, 2012). Recentemente um grupo identificou que apenas cerca de 8% das variantes no LDLR identificadas no banco de dados ClinVar são completamente caracterizadas por estudos in vitro (CHORA et al, 2018).…”