ClinVar Genomic variation as it relates to human health

NM_000527.4(LDLR): c.1049G>C (p.Arg350Pro) variant is classified as Likely Pathogenic for Familial Hypercholesterolemia by applying evidence codes PM2, PS4_Supporting, PP1_Moderate, PP4, and PS3 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: . PM2: This variant is absent from gnomAD (gnomAD v2.1.1). . PS4_Supporting: Variant meets PM2 and is identified in 5 index cases: 4 cases with DLCN criteria>=6 from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA), 1 case with DLCN criteria>=6 in Service de Biochimie et de Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France . PP1_Moderate: Variant segregates with FH phenotype in 5 informative meioses in 3 families from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA). 3 relatives without the phenotype and the variant, 2 relatives with the phenotype and the variant . PP4: Variant meets PM2 and is identified in at least 1 index case with DLCN>=6 after alternative causes of high cholesterol were excluded. Data is from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA) and Service de Biochimie et de Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France. . PS3_moderate: Level 2 assays: PMID 15100232 Heterologous cells (CHO) ACS, WB and NMR Spectroscopy <10% cell surface LDLR, 65% binding, (WB), ~10% expression

LDLR p.Arg350Pro (originally Arg329Pro, FH Alghero) missense variant has previously been identified in multiple cohorts of familial hypercholesterolemia patients. In vitro studies demonstrated that LDLR p.Arg350Pro affected protein folding and surface expression, resulting in decreased LDL-receptor activity (PMID: 15100232, 9026534).

Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate that this variant results in protein misfolding and reduced cell-surface expression compared to the wild-type protein (Boswell et al., 2004) as well as results in impaired binding interaction with PCSK9 (Gu et al., 2013); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.R329P; This variant is associated with the following publications: (PMID: 17094996, 31106925, 9026534, 24103783, 19837725, 15556093, 11435110, 32719484, 22883975, 15100232)

The LDLR c.1049G>C (p.Arg350Pro) variant has been reported in the published literature in multiple individuals with familial hypercholesterolemia including at least one case with another LDLR variant (p.Cys248Tyr) in trans (PMIDs: 9026534 (1996), 17094996 (2007), and 22883975 (2012)). Experimental studies have shown that this variant results in protein misfolding, reduced cell-surface expression, decreased LDL-receptor activity (PMIDs: 9026534 (1996) and 15100232 (2004)), and impaired binding interaction with PCSK9 (PMID: 24103783 (2013)). The frequency of this variant in the general population, 0.0000066 (1/152190 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as likely pathogenic.

This missense variant (also known as p.Arg329Pro in the mature protein) replaces arginine with proline at codon 350 in the EGF-like repeat A of the EGF precursor homology domain of the LDLR protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Experimental functional studies have shown that this variant causes LDLR protein misfolding and significant reduction in protein activity (PMID: 9026534, 15100232). This variant has been reported in one individual affected with familial hypercholesterolemia (PMID: 31106925). This variant has also been reported in compound heterozygosity with a pathogenic variant p.Cys248Tyr in an individual affected with familial hypercholesterolemia (PMID: 9026534). The proband's affected sister was also compound heterozygous. The proband's affected father was heterozygous for this variant, and the proband's affected mother was heterozygous for p.Cys248Tyr (PMID: 9026534). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). In summary, this rare variant has been shown to disrupt LDLR function and demonstrated to segregate with disease in a family study. Based on available evidence, this variant is classified as Likely Pathogenic.

This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 350 of the LDLR protein (p.Arg350Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with familial hypercholesterolemia (PMID: 9026534, 19837725; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 226343). 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. Experimental studies have shown that this missense change affects LDLR function (PMID: 15100232). This variant disrupts the p.Arg350 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been observed in individuals with LDLR-related conditions (PMID: 31106925), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.

The p.R350P variant (also known as c.1049G>C and p.R329P), located in coding exon 7 of the LDLR gene, results from a G to C substitution at nucleotide position 1049. The arginine at codon 350 is replaced by proline, an amino acid with dissimilar properties. This variant has been reported in individuals with hypercholesterolemia, including two siblings with severe hypercholesterolemia who had a second LDLR variant in trans (Ambry internal data; Hendry WG et al. J R Soc Med, 1985 Apr;78:334-5; Webb JC et al. J Lipid Res, 1996 Feb;37:368-81; Tosi I et al. Atherosclerosis, 2007 Sep;194:102-11; Hooper AJ et al. Atherosclerosis, 2012 Oct;224:430-4). This alteration was also detected in one individual from a cohort of 29,906 healthy individuals who underwent multigene panel testing (Grzymski JJ et al. Nat Med, 2020 08;26:1235-1239). One functional study demonstrated reduced cell surface expression of LDLR, which was attributed to protein misfolding (Boswell EJ et al. J Biol Chem, 2004 Jul;279:30611-21). Based on internal structural analysis, p.R350P is deleterious (Lo Surdo P et al. EMBO Rep, 2011 Dec;12:1300-5; Ambry internal data). This amino acid position is poorly conserved in available vertebrate species. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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.