The NM_000527.5(LDLR):c.907C>T (p.Arg303Trp) variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes (PP3) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1101/2021.03.17.21252755). The supporting evidence is as follows: PP3 - REVEL = 0.815. It is above 0.75, so PP3 is Met.

The p.R303W variant (also known as c.907C>T), located in coding exon 6 of the LDLR gene, results from a C to T substitution at nucleotide position 907. The arginine at codon 303 is replaced by tryptophan, an amino acid with dissimilar properties. This variant (also referred to as R282W) has been detected in cohorts with hypercholesterolemia; however, in several cases, clinical details were limited, and, in one case, it co-occurred with another variant in LDLR (Arca M. Atherosclerosis. 1998 Jan;136(1):187-94; Pirillo A et al. Atheroscler Suppl, 2017 Oct;29:17-24; Lange LA et al. Am. J. Hum. Genet., 2014 Feb;94:233-45; Sun YV et al. Circ Genom Precis Med, 2018 12;11). This variant has also been detected in an early onset myocardial infarction (MI) cohort and MI-free controls, as well as in a low LDL-C and healthy exome cohorts (Do R et al. Nature, 2015 Feb;518:102-6; Lange LA et al. Am. J. Hum. Genet., 2014 Feb;94:233-45; Amendola LM et al. Genome Res., 2015 Mar;25:305-15; Grzymski JJ et al. Nat Med, 2020 08;26:1235-1239). This alteration impacts a residue in the conserved cluster of acidic amino acids at the C-terminal end of LDLR class A repeat 7 (Jeon H and Blacklow C. Annu. Rev. Biochem. 2005;74:535-62). Based on data from gnomAD, the frequency for this variant is above the maximum credible frequency for a disease-causing variant in this gene based on internally established thresholds (Karczewski et al. Nature. 2020 May;581(7809):434-443; Whiffin et al. Genet Med. 2017 10;19:1151-1158). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear.

This missense variant replaces arginine with tryptophan at codon 303 of the LDLR protein. This variant is also known as p.Arg282Trp in the mature protein. This variant alters a conserved arginine residue in the LDLR type A repeat 7 of the LDLR protein (a.a. 274-314), where pathogenic missense variants are found enriched (ClinVar-LDLR). Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with familial hypercholesterolemia (PMID: 9544746, 28965616, 31345425, 34040191). This variant has also been observed in compound heterozygous state in individuals affected with homozygous familial hypercholesterolemia (PMID: 32977124, 36507290). This variant has been identified in 13/282676 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

The LDLR c.907C>T (p.Arg303Trp) variant has been reported in the published literature in individuals with familial hypercholesterolemia (FH) (PMID: 9544746 (1998), 25637381 (2015), 28965616 (2017), 31106297 (2018), 31345425 (2019), 33079599 (2020), 33955087 (2021), 34040191 (2021), 35741760 (2022), and 36184534 (2022)). It has also been described in individuals with homozygous familial hypercholesterolemia (hoFH) (PMIDs: 32977124 (2020) and 36507290 (2022)), as well as in an individual with early age myocardial infarction (PMID: 25487149 (2015)).The frequency of this variant in the general population (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, we are unable to determine the clinical significance of this variant.

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(R282W); This variant is associated with the following publications: (PMID: 25637381, 25487149, 31106297, 32977124, 32719484, 33955087, 24507775, 35741760, 34040191, 36507290, 28965616, 9544746, 37409534)

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 303 of the LDLR protein (p.Arg303Trp). This variant is present in population databases (rs151207122, gnomAD 0.04%). This missense change has been observed in individuals with hypercholesterolemia (PMID: 9544746, 24507775, 28965616, 34040191; internal data). This variant is also known as p.Arg282Trp and R282W. ClinVar contains an entry for this variant (Variation ID: 161281). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt LDLR protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

PP3

Variant summary: LDLR c.907C>T (p.Arg303Trp) results in a non-conservative amino acid change located in the Low-density lipoprotein (LDL) receptor class A repeat of the encoded protein sequence. Algorithms developed to predict the effect of missense changes on protein structure and function all suggest that this variant is likely to be disruptive. The variant allele was found at a frequency of 4.8e-05 in 251326 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in LDLR causing Familial Hypercholesterolemia (4.8e-05 vs 0.0013), allowing no conclusion about variant significance. c.907C>T has been reported in the literature in individuals affected with Familial Hypercholesterolemia (Arca_1997, Pirillo_2017, Ajufo_2021, Rutkowska_2022, Okada_2022, Young__2022, Benedek_2021, LCG internal data). The Arg303 codon and adjacent codons (p.303Q p.C302R, p.C302W, p.D304N, p.D304E) have been implicated in Familial Hypercholesterolemia, suggesting the codon and region may be a mutational hotspot and critical for protein function. These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 34040191, 25637381, 9544746, 32977124, 34906454, 25487149, 24507775, 36184534, 28965616, 35741760, 31106297, 36229376, 33079599, 31345425, 36507290, 33955087). ClinVar contains an entry for this variant (Variation ID: 161281). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

This missense variant replaces arginine with tryptophan at codon 303 of the LDLR protein. This variant is also known as p.Arg282Trp in the mature protein. This variant alters a conserved arginine residue in the LDLR type A repeat 7 of the LDLR protein (a.a. 274-314), where pathogenic missense variants are found enriched (ClinVar-LDLR). Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with familial hypercholesterolemia (PMID: 9544746, 28965616, 31345425, 34040191). This variant has also been observed in compound heterozygous state in individuals affected with homozygous familial hypercholesterolemia (PMID: 32977124, 36507290). This variant has been identified in 13/282676 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.