ClinVar Genomic variation as it relates to human health

The NM_000527.5 (LDLR): c.2113G>T (p.Ala705Ser) variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes (PM2, PP4, PS4_Supporting) 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 Met: PopMAX MAF = 0.00004 in European (Non-Finnish) population in gnomAD (gnomAD v2.1.1). PP4 Met: This variant meets PM2 and is identified in >1 index cases who met clinical criteria for FH after alternative causes for high cholesterol were excluded. PS4_Supporting Met: Variant meets PM2 and is identified in 2 unrelated index cases who fulfil DLCN criteria or Simon Broome criteria for FH from 2 different labs: 1 case met DLCN criteria from Robarts Research Institute, Canada; 1 case met Simon Broome criteria from Centre for Cardiovascular Genetics, British Heart Foundation Laboratories, Royal Free and University College London Medical School, London, UK, PMID 17142622. PP3 not met: REVEL score = 0.673, which is below the threshold of 0.75. Functional data on splicing is not available, in silico splicing prediction is required. Variant is exonic and at least 50bp downstream from acceptor site and creates GT. MES scores: de novo donor = -6.49, authentic donor = 7.81. De novo score is negative and not used, therefore the variant is not predicted to alter splicing. BP4 not applicable: REVEL score is > 0.5, therefore BP4 is not applicable. PS3 not met: There is no functional experiment reported for this variant. PM5 not met: There is one other variant in the same codon: LDLR: NM_000527:c.2113G>C (p.Ala705Pro) is classified as Uncertain significance - insufficient evidence by these guidelines. Therefore PM5 is not met.

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. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts the p.Ala705 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 11810272, 18325082, 21382890, 22095935, 23375686, 25412742). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 252224). This variant is also known as A684S. This missense change has been observed in individual(s) with combined hyperlipidemia and/or familial hypercholesterolemia (PMID: 15556093, 33303402). This variant is present in population databases (rs193922570, gnomAD 0.004%). This sequence change replaces alanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 705 of the LDLR protein (p.Ala705Ser).

This missense variant (also known as p.Ala684Ser in the mature protein) replaces alanine with serine at codon 705 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). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with familial hypercholesterolemia (PMID: 15556093, 18325082) and in an individual affected with hyperlipidemia (PMID: 33303402). This variant has been identified in 5/250870 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 p.A705S variant (also known as c.2113G>T), located in coding exon 14 of the LDLR gene, results from a G to T substitution at nucleotide position 2113. The alanine at codon 705 is replaced by serine, an amino acid with similar properties. This alteration has been reported in subjects with familial hypercholesterolemia (FH) (Humphries SE et al. J Med Genet, 2006 Dec;43:943-9; Sozen M et al. Atheroscler Suppl, 2004 Dec;5:7-11; Whittall RA et al. Ann Clin Biochem, 2010 Jan;47:44-55; Gill PK et al. J Clin Lipidol, 2021 Nov;15:79-87). 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 limited at this time, the clinical significance of this alteration remains unclear.

Variant summary: LDLR c.2113G>T (p.Ala705Ser) results in a conservative amino acid change located in the EGF-like domain (IPR000742) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2e-05 in 250870 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.2113G>T has been reported in the literature in the heterozygous state in at least 1 individual affected with Familial Hypercholesterolemia (example, Gill_2021, Guerin_2023, Leigh_2008). These report(s) do not provide unequivocal conclusions about association of the variant with Familial Hypercholesterolemia. 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: 33303402, 37607748, 18325082). ClinVar contains an entry for this variant (Variation ID: 252224). Based on the evidence outlined above, the variant was classified as uncertain significance.