ClinVar Genomic variation as it relates to human health

The NM_000527.5 (LDLR): c.2113G>C (p.Ala705Pro) variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes (PM2, PP4, PP3) 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 = 0.00001 in European (Non-Finnish) population in gnomAD (gnomAD v2.1.1). PP4 Met: This variant meets PM2 and is identified in 1 index case who met clinical criteria for FH after alternative causes for high cholesterol were excluded (Department of Vascular Medicine, Academic Medical Center at the University of Amsterdam, Amsterdam, The Netherlands, PMID 11810272). PP3 Met: REVEL score = 0.78, which is above the threshold of 0.75. 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>T (p.Ala705Ser) is classified as Uncertain significance - insufficient evidence by these guidelines. Therefore PM5 is not met.

This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 705 of the LDLR protein (p.Ala705Pro). This variant is present in population databases (rs193922570, gnomAD 0.0009%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 11810272, 18325082, 21382890, 22095935, 23375686, 25412742). This variant is also known as p.A684P. ClinVar contains an entry for this variant (Variation ID: 36459). 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%. This variant disrupts the p.Ala705 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been observed in individuals with LDLR-related conditions (PMID: 15556093), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.

Identified in many individuals with FH referred for genetic testing at GeneDx and in published literature (PMID: 11810272, 18325082, 20506408, 21382890, 23375686, 23833242); A large study of individuals from the Netherlands with FH-related variants concluded that LDL-C levels were significantly higher in p.(A705P) carriers compared to non-carriers (PMID: 20506408); 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.(A684P); This variant is associated with the following publications: (PMID: 18325082, 21382890, 23375686, 22390909, 21642693, 22095935, 23833242, 27919364, 23369702, 25412742, 20506408, 11810272, 34037665, 32719484)

Variant summary: The c.2113G>C (p.Ala705Pro) in LDLR gene is a missense variant involves a highly conserved nucleotide and 2/4 in silico tools (SNPsandGO not captured here due to low reliability index value) predict deleterious outcome. However, no functional studies supporting these predictions were published at the time of evaluation. The c.2113G>C is present in the control population dataset of gnomAD at a low frequency of 0.000004 (1/245716 chromosomes tested). The observed frequency does not exceed the maximum expected allele frequency for a pathogenic variant of 0.0012, suggesting that it is not a common polymorphism. The variant has been reported in multiple affected individuals with FH, including one patient, who carried R3500Q in APOB with lipid profile suggestive of being a carrier of two pathogenic variants. The variant reportedly classified as having a delayed (2B) transport from the endoplasmic reticulum to the cell surface, but is cited as VUS by reputable databases/clinical laboratories. Lastly, the codon Ala705 appears to be a hot spot, and another alteration, c.2113G>T (p.Ala705Ser) has been reported in association with Hypercholesterolaemia. Taken together the variant was classified as Pathogenic.

The p.A705P pathogenic mutation (also known as c.2113G>C), located in coding exon 14 of the LDLR gene, results from a G to C substitution at nucleotide position 2113. The alanine at codon 705 is replaced by proline, an amino acid with highly similar properties. This alteration, also referred to as A684P, has been detected in multiple individuals from Dutch familial hypercholesterolemia (FH) cohorts with elevated mean LDL-C level compared to controls; however, in some cases, clinical details were limited (Fouchier SW et al. Hum Genet. 2001;109:602-15; Huijgen R et al. Circ Cardiovasc Genet. 2011;4:413-7; van der Graaf A et al. Circulation. 2011;123:1167-73). This alteration was also seen in an Italian FH cohort (Bertolini S et al. Atherosclerosis. 2013;227:342-8). In one family, this alteration segregated with hypercholesterolemia in two individuals, but was also detected in two relatives without elevated cholesterol (Huijgen R et al. Hum Mutat. 2012;33:448-55). In another report, this alteration was seen in conjunction with an APOB mutation in a patient with untreated LDL-C level of 9.6mmol/L (Sjouke B et al. J Clin Lipidol. 2016;10:1462-1469). Another alteration affecting this amino acid (p.A705S) has also been detected in an FH cohort (Humphries SE. J Med Genet. 2006;43(12):943-9). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.