0/190 non-FH alleles

Disrupt disulfide bridge between Cys216 and Cys231.

Variant summary: LDLR c.691T>G (p.Cys231Gly) results in a non-conservative amino acid change located in the fifth class A repeat (IPR002172) of the encoded protein sequence. The class A repeats form the binding sites for LDL and contain six cysteine residues involved in disulfide bond formation that are required for structural integrity (InterPro). Numerous missense changes affecting cysteine residues within LDLR class A repeats are found among patients with hypercholesterolemia (HGMD), in addition, other variants affecting the same residue (Cys231), have been reported in affected individuals (HGMD). 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 4.1e-06 in 246490 control chromosomes (gnomAD). The variant, c.691T>G (aka. C210G), has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia (e.g. Heath_2001, Tichy_2012, Leren_2021), and was described as a frequent founder variant in Norwegian FH patients (Leren_2021). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014, and all laboratories classified the variant as pathogenic (n=2) / likely pathogenic (n=3). Based on the evidence outlined above, the variant was classified as pathogenic.

The p.C231G pathogenic mutation (also known as c.691T>G), located in coding exon 4 of the LDLR gene, results from a T to G substitution at nucleotide position 691. The cysteine at codon 231 is replaced by glycine, an amino acid with highly dissimilar properties. This alteration (also referred to as p.C210G) has been reported in multiple individuals with familial hypercholesterolemia (FH), commonly occurring in Norwegian FH cohorts (Sundvold H et al. Hum Mutat. 1996;7:70-1; Heath KE et al. Eur J Hum Genet. 2001;9:244-52; Dušková L et al. Atherosclerosis. 2011;216:139-45; Tichý L et al. Atherosclerosis. 2012;223(2):401-8). Other variants at the same codon (including p.C231R, c.691T>C and p.C231W, c.693C>G) have also been reported in association with FH (Wang L et al. Nutr Metab Cardiovasc Dis. 2009;19(6):391-400; Marduel M et al. Hum Mutat. 2010;31(11):E1811-24). Pathogenic LDLR mutations that result in the substitution or generation of cysteine residues within the cysteine-rich LDLR class A repeats and EGF-like domains are common in familial hypercholesterolemia (FH) (Villéger L. Hum Mutat. 2002;20(2):81-7). Internal structural analysis indicates this variant eliminates a disulfide bond critical for the structural integrity of the LDLR class A repeat 5 domain (Ambry internal data). 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 supporting evidence, this variant is interpreted as a disease-causing mutation.

Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies in transfected LDL-deficient CHO cells showed the p.(C231G) variant had near normal expression, but only 30-40% activity in both the 24- and 96-well assays (PMID: 37719435); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(C210G); This variant is associated with the following publications: (PMID: 11313767, 33955087, 33508743, 38258479, 22698793, 33740630, 10422804, 21310417, 8664907, 37719435)

The LDLR c.691T>G (p.Cys231Gly) variant has been reported in the published literature in several individuals and families with familial hypercholesterolemia (FH) (PMIDs: 33955087 (2021), 33740630 (2021), 31893465 (2020), 22698793 (2012), 21310417 (2011), 11313767 (2001), 8664907 (1996)). Assessment of experimental analysis yielded inconclusive results regarding the impact of this variant on protein function (PMID: 37719435 (2023)). Multiple missense variants at this codon, including at least one considered to be pathogenic or likely pathogenic, have been reported in individuals with clinical features associated with this gene, suggesting this variant may also cause disease (PMIDs: 19073363 (2009), 10782930 (2000)). 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, this variant is classified as pathogenic.

PS4,PM1,PM2,PP3

This sequence change replaces cysteine, which is neutral and slightly polar, with glycine, which is neutral and non-polar, at codon 231 of the LDLR protein (p.Cys231Gly). This variant is present in population databases (rs746091400, gnomAD 0.006%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 10422804, 11313767, 22698793). This variant is also known as C210G. ClinVar contains an entry for this variant (Variation ID: 251397). 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%. This variant affects a cysteine residue located within an LDLRA or epidermal-growth-factor (EGF)-like domains of the LDLR protein. Cysteine residues in these domains have been shown to be involved in the formation of disulfide bridges, which are critical for protein structure and stability (PMID: 7548065, 7603991, 7979249). In addition, missense substitutions within the LDLRA and EGF-like domains affecting cysteine residues are overrepresented among patients with hypercholesterolemia (PMID: 18325082). This variant disrupts the p.Cys231 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been observed in individuals with LDLR-related conditions (PMID: 10422804, 10782930, 19073363), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.