ClinVar Genomic variation as it relates to human health

Disrupt disulfide bridge between Cys318 and Cys329.

The LDLR c.986G>A; p.Cys329Tyr variant (rs761954844), also known as Cys308Tyr, is reported in the literature in multiple individuals and families affected with familial hypercholesterolemia (Alver 2019, Mak 1998, Miroshnikova 2021, Jiang 2015). Functional analyses show the variant protein had LDLR activity of ~30% of wildtype (Jiang 2015). This variant is reported in ClinVar (Variation ID: 226344) and is found in the general population with an overall allele frequency of 0.003% (7/282402 alleles) in the Genome Aggregation Database. The cysteine at codon 329 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.965). Based on available information, this variant is considered to be pathogenic. References: Alver M et al. Recall by genotype and cascade screening for familial hypercholesterolemia in a population-based biobank from Estonia. Genet Med. 2019 May;21(5):1173-1180. PMID: 30270359. Mak YT et al. Possible common mutations in the low density lipoprotein receptor gene in Chinese. Hum Mutat. 1998;Suppl 1:S310-3. PMID: 9452118. Miroshnikova VV et al. Identification of novel variants in the LDLR gene in Russian patients with familial hypercholesterolemia using targeted sequencing. Biomed Rep. 2021 Jan;14(1):15. PMID: 33269076. Jiang L et al. The distribution and characteristics of LDL receptor mutations in China: A systematic review. Sci Rep. 2015 Nov 26;5:17272. PMID: 26608663.

The p.Cys329Tyr variant in LDLR has been reported in at least 25 individuals (including 17 Taiwanese, 2 Russian, 2 Chinese, 1 Filipino, and 1 Czech individuals) with Familial Hypercholesterolemia (PMID: 22353362, 9763532, 11810272, 15701167, 16205024, 27765764, 22698793), and has been identified in 0.01003% (2/19938) of East Asian chromosomes and 0.005645% (2/35428) of Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs761954844). Please note that for diseases with clinical variability, or reduced penetrance, pathogenic variants may be present at a low frequency in the general population. This variant has also been reported as a likely benign variant, likely pathogenic variant, and pathogenic variant in ClinVar (Variation ID: 226344). In vitro functional studies with transfected COS cells provide some evidence that the p.Cys329Tyr variant may impact LDL receptor activity (PMID: 26608663). 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. One additional variant with a different amino acid change at the same position (p.Cys329Phe) has been reported in association with disease in ClinVar, supporting that a change at this position may not be tolerated (Variation ID: 251586). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic. ACMG/AMP Criteria applied: PS4, PS3_supporting, PM5_supporting, PP3 (Richards 2015).

This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 329 of the LDLR protein (p.Cys329Tyr). This variant is present in population databases (rs761954844, gnomAD 0.01%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 9452118, 30270359, 30592178, 31706281). It has also been observed to segregate with disease in related individuals. This variant is also known as C308Y. ClinVar contains an entry for this variant (Variation ID: 226344). 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%. For these reasons, this variant has been classified as Pathogenic.

The c.986G>A (p.C329Y) alteration is located in exon 7 (coding exon 7) of the LDLR gene. This alteration results from a G to A substitution at nucleotide position 986, causing the cysteine (C) at amino acid position 329 to be replaced by a tyrosine (Y). Based on data from gnomAD, the A allele has an overall frequency of 0.003% (7/282402) total alleles studied. The highest observed frequency was 0.01% (2/19938) of East Asian alleles. This alteration, also referred to as p.C308Y, has been described in multiple individuals with familial hypercholesterolemia (FH) (Mak, 1998; Fouchier, 2001; Punzalan, 2005; Zakharova, 2005; Chiou, 2010; Tichý, 2012; Fan, 2015). This alteration has also been reported to segregate with the disease in one family, and in vitro studies suggested that the alteration led to reduced surface protein expression and ligand binding (Chang, 2003). 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 FH (Villéger, 2002). Structural analysis indicates this alteration eliminates a disulfide bond critical for the structural integrity of the EGF-like 1 domain (Ambry internal data). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

Based on the ACMG/AMP 2015 guidelines (Richards 2015), p.Cys329Tyr variant has the following pathogenicity criteria: PS3 - an in vitro functional study shows that the presence of this variant reduces LDL receptor activity to 31% in transfected COS cells (Chang 2003); PM1 - located in a critical and well-established functional domain of the LDLR (EGF-A) (Galicia-Garcia 2020); PM2 - detected in control samples of gnomAD v4.1.0 with a frequency of 0.0006197%; PP1 - segregated with FH in 4 relatives in 2 families (data from the Laboratory of Molecular Genetics, Moscow, Russia); PP3; PP4 (registered in patients with FH). According to the ClinGen guidelines for LDLR variant classification (Chora 2022): PS4 - variant is found in ≥10 unrelated FH cases, including in Russia (Jiang 2015 (n = 26), Meshkov 2021 and Vasilyev 2022 (n = 13)); PS3_Moderate - meets level 2 pathogenic functional study criteria (Chang 2003); PM1 - changes in 1 of 60 highly conserved cysteine residues (p.Cys329) (Chora 2022); PM2 - has a PopMax MAF ≤ 0.0002 (0.02%) in gnomAD (0.0006197% v4.1.0 gnomAD); PP1_Moderate - segregates with phenotype in 4 informative meioses in 2 family (data from the Laboratory of Molecular Genetics, Moscow, Russia); PP3 - REVEL score 0.965 (Liu 2011, Liu 2020); PP4 - identified in 8 probands with FH (diagnosis based on DLCN-criteria (Meshkov 2021)). Based on a combination of criteria, this variant is pathogenic.

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 p.(C308Y); This variant is associated with the following publications: (PMID: 31706281, 30592178, 33269076, 32423031, 30270359, 32041611, 33303402, 33740630, 33994402, 9452118)

subject mutated among 2600 FH index cases screened = 1 / previously described in association with FH (linked to ethnicity ?) / Software predictions: Damaging