ClinVar Genomic variation as it relates to human health

The NM_000527.5(LDLR):c.226G>T (p.Gly76Trp) variant is classified as Uncertain significance - conflicting evidence for Familial Hypercholesterolemia by applying evidence codes BS3, PS4_Supporting, PM2, PP1_Moderate, and PP4 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: BS3: Level 1 assays: PMID 25741862: Heterologous cells (CHO), western blot and flow cytometry assays - result: 100% low-density lipoprotein particle receptor biosynthetic process; 90% low-density lipoprotein particle binding; 95% low-density lipoprotein particle clearance. ---- The whole cycle is above 90% of wild-type activity. So, BS3 is met. PS4_Supporting: Variant meets PM2 and is identified in 2 index cases (1 case with DLCN criteria of definite FH from U4M - Lille University & CHRU Lille and 1 case with Simon Broome criteria of possible FH from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge). So, PS4_Supporting is met. PM2: This variant is absent from gnomAD (gnomAD v2.1.1). So, PM2 is met. PP3: REVEL=0.898. It is above 0.75, so PP3 is met. PP1_Moderate: Variant segregates with FH phenotype in 4 informative meioses in 1 family from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge. So, PP1_Moderate is met. PP4: Variant meets PM2 and is identified in 2 unrelated index cases who fulfill clinical criteria for FH from different labs, after alternative causes of high cholesterol were excluded (see PS4 for details). So, PP4 is met.

0/100 normolipidemic individuals

subject mutated among 2600 FH index cases screened = 1 , family member = 1 with co-segregation / mild phenotype / Software predictions: Damaging

The p.Gly76Trp variant in LDLR has been reported in at least 1 Portuguese individual with familial hypercholesterolemia (PMID: 17765246), and was absent from large population studies. This variant has also been reported in ClinVar as having conflicting interpretations of pathogenicity (Variation ID: rs574337291). In vitro functional studies provide some evidence that the p.Gly76Trp variant may not impact protein function (PMID: 25741862). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of the p.Gly76Trp variant is uncertain. ACMG/AMP Criteria applied: PM2, PP3, BS3_supporting (Richards 2015).

The p.G76W variant (also known as c.226G>T), located in coding exon 3 of the LDLR gene, results from a G to T substitution at nucleotide position 226. The glycine at codon 76 is replaced by tryptophan, an amino acid with highly dissimilar properties. This alteration has been reported in a familial hypercholesterolemia (FH) cohort with limited clinical details and in a cohort of 29,906 healthy individuals who underwent multigene panel testing (Bourbon M et al. Atherosclerosis, 2008 Feb;196:633-42; Grzymski JJ et al. Nat Med, 2020 08;26:1235-1239). An in vitro assay showed this alteration may not impact protein function (Benito-Vicente A et al. Genet Med, 2015 Dec;17:980-8). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

Identified in a patient with familial hypercholesterolemia (FH) in published literature (PMID: 17765246); Not observed at significant frequency in large population cohorts (gnomAD); A published functional study suggests the p.(G76W) showed similar levels of expression and trafficking to cell surface compared to wildtype (PMID: 25741862); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(G55W); This variant is associated with the following publications: (PMID: 32719484, 29261184, 29874871, 27821657, 22881376, 17765246, 25741862)