ClinVar Genomic variation as it relates to human health

The NM_000527.5 (LDLR):c.1474G>C (p.Asp492His) variant is classified as Likely Pathogenic for Familial Hypercholesterolemia by applying ACMG/AMP evidence codes PM2, PM5, PP3 and PP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (specification version 1.2) on 7 November 2023. The supporting evidence is as follows: PM2: PopMax MAF=0.00002 in Non-Finnish European population in gnomAD (gnomAD v2.1.1). PP3: REVEL=0.993. PM5: Two other missense variants in the same codon: NM_000527.5(LDLR):c.1474G>A (p.Asp492Asn), ClinVar 161285, classified as Pathogenic by these guidelines; NM_000527.5(LDLR):c.1475A>G (p.Asp492Gly), ClinVar 251865, classified as Likely Pathogenic by these guidelines. Therefore PM5 is met. PP4: Variant meets PM2 and is identified in 1 index case who fulfils Simon Broome criteria for FH diagnosis after alternative causes of high cholesterol were excluded, reported in PMID 10208479 (Heath et al., 1999), from University College London Medical School, UK.

This missense variant (also known as p.Asp471His in the mature protein) is located in the LDLR type B repeat 3 of the EGF precursor homology domain of the LDLR protein. This variant changes a highly conserved Asp residue within the functionally important YWTD motif. Computational prediction tools and conservation analyses suggest that this variant may have deleterious impact on the protein function. Computational splicing tools suggest that this variant may not impact the RNA splicing. To our knowledge, functional assays have not been performed for this variant. This variant has been reported in individuals affected with familial hypercholesterolemia in UK (PMID: 10208479, 15556093, 16389549, 31993549). This variant has been identified in 2/277190 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different missense variants at the same position (p.Asp492Asn and p.Asp492Gly) are considered to be disease-causing. Based on available evidence, this variant is classified as Likely Pathogenic.

Variant summary: LDLR c.1474G>C (p.Asp492His) results in a non-conservative amino acid change located in the LDLR class B repeat domain (IPR000033) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.9e-06 in 258942 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1474G>C has been reported in the literature in individuals affected with Familial Hypercholesterolemia (Heath_1999, Khera_2019). In addition, other missense changes at this position, p.Asp492Asn and p.Asp492Gly, and nearby codons, p.Thr491Asn, p.Gly496Asp, p.Gly496Val, p.Thr497Pro, have been reported as pathogenic, suggesting this region is important for protein function. Furthermore, Jeon_2001, reports that mutations in this region are likely to disrupt the structure of the propeller and prevent efficient transport of the receptor to the cell surface leading to Familial Hypercholesterolemia. These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and a predominant consensus as pathogenic/likely pathogenic (n=3) (VUS, n=1). Most submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as likely pathogenic.

The LDLR c.1474G>C (p.Asp492His) variant has been reported in the published literature in affected individuals and families with familial hypercholesterolemia or early-onset myocardial infarction (PMIDs: 16389549 (2006), 10208479 (1999), 30586733 (2019), 31993549 (2020), and 34037665 (2021)). The frequency of this variant in the general population, 0.0000071 (2/282806 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as likely pathogenic.

This sequence change replaces aspartic acid, which is acidic and polar, with histidine, which is basic and polar, at codon 492 of the LDLR protein (p.Asp492His). This variant is present in population databases (no rsID available, gnomAD 0.002%). This missense change has been observed in individuals with clinical features of familial hypercholesterolemia (PMID: 10208479; Invitae). This variant is also known as p.Asp471His (D471H). ClinVar contains an entry for this variant (Variation ID: 251864). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt LDLR protein function with a positive predictive value of 95%. This variant disrupts the p.Asp492 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9763532, 10230472, 16250003, 23375686, 25487149, 25936317). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

PP3, PM2_supporting, PM5, PS4_moderate

The p.D492H variant (also known as c.1474G>C), located in coding exon 10 of the LDLR gene, results from a G to C substitution at nucleotide position 1474. The aspartic acid at codon 492 is replaced by histidine, an amino acid with similar properties. This variant, historically known as p.D471H, has been reported in familial hypercholesterolemia (FH) and early onset myocardial infarction (MI) cohorts (Heath KE et al. Atherosclerosis, 1999 Mar;143:41-54; Sozen M et al. Atheroscler Suppl, 2004 Dec;5:7-11; Khera AV et al. Circulation, 2019 Mar;139:1593-1602; Sturm AC et al. JAMA Cardiol, 2021 08;6:902-909). Alterations affecting the same amino acid (p.D492N and p.D492G) have also been described in association with FH (Mak YT et al. Arterioscler. Thromb. Vasc. Biol., 1998 Oct;18:1600-5; Fouchier SW et al. Hum. Mutat., 2005 Dec;26:550-6). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

Also reported in a patient with early-onset myocardial infarction; however, additional clinical data including cholesterol levels were not provided (PMID: 30586733); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as D471H; This variant is associated with the following publications: (PMID: 15556093, 30586733, 32719484, 34037665, 10208479, 11373616, 16389549, 11313767)