Submissions for variant NM_000527.5(LDLR):c.718G>A (p.Glu240Lys)

gnomAD frequency: 0.00004  dbSNP: rs768563000

Total submissions: 20

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	RCV000211564	SCV002506368	pathogenic	Hypercholesterolemia, familial, 1	2022-02-14	reviewed by expert panel	curation	The NM_000527.5(LDLR):c.718G>A (p.Glu240Lys) variant is classified as U Pathogenic for Familial Hypercholesterolemia by applying evidence codes PP3, PM2, PS4, PM3, 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: PP3 - REVEL = 0.865. It is above 0.75, so PP3 is Met. PM2 - PopMax MAF = 0.00005418 (0.005418%) in European (non-Finnish) exomes+genomes (gnomAD v2.1.1), so PM2 is Met. PS4 - Variant meets PM2 and is identified in at least 11 unrelated index cases: 2 index cases with Simon Broome possible from Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière); 1 index case with DLCN>6 from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA); 2 index cases with DLCN>6 from Robarts Research Institute; 2 index cases with DLCN>6 from Color Health, Inc; 2 index cases fulfilling the following criteria: children with a) TC >200 mg/dl or LDL >120 mg/dl and b) presence of primary hypercholesterolemia in 1st degree relatives with autosomal dominant mode of inheritance or c) family history of pCHD or d) presence of xanthomas in proband or in parents, from Greece (PMID: 25463123); at least 1 index case with Simon Broome criteria from China (PMID: 28235710); 1 index case with Definite FH (LDL >13 mmol/l and presence of xanthomas and hypercholesterolemia in both parents) from Italy (PMID: 32977124), so PS4 is Met. PM3 - Variant meets PM2 and is identified in an italian index case with homozygous FH phenotype (LDL>13 mmol/l) with another LDLR variant, in trans (PMID: 32977124). In PMID: 28965616 is identified an italian index case (phenotype not reported) with LDLR variant c.304C>T (p.Gln102*), classified as Pathogenic by these guidelines, but cannot determine if the variants are in trans (PMID: 28965616). Assuming that is the same homozygous index case (same lab), PM3 is Met. PP4 - Variant meets PM2 and is identified in at least 11 unrelated index cases as reported above, so PP4 is Met.
GeneDx	RCV000182341	SCV000234645	pathogenic	not provided	2022-03-12	criteria provided, single submitter	clinical testing	Published functional studies show that an individual who harbors the E240K variant as well as a different benign variant in the LDLR gene exhibits receptor activity 15-30% of wild type receptor activity (Hobbs et al., 1992).; Biochemical experiments provide preliminary evidence that this variant gives rise to a protein folding defect (North and Blacklow, 2000a; North and Blacklow, 2000b); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24956927, 28008010, 16250003, 19062533, 1301956, 23375686, 28235710, 28965616, 10704205, 30293248, 19118540, 25463123, 11052664, 21990180, 18929537, 31401775, 30241732, 31947532, 31447099, 32977124, 32041611, 33303402, 32719484, 34037665)
Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital	RCV000211564	SCV000268584	likely pathogenic	Hypercholesterolemia, familial, 1	2022-01-05	criteria provided, single submitter	clinical testing	The LDLR p.Glu240Lys (originally p.Glu219Lys, FH Charlotte) missense variant is likely pathogenic for familial hypercholesterolaemia (FH). In silico algorithms (PolyPhen2, SIFT, MutationTaster) predict p.Glu240Lys to be pathogenic. It has previously been identified in multiple cohorts of FH patients worldwide and is present at a very low frequency (2/121,396 alleles) in the gnomAD population database. In vitro studies demonstrated that LDLR p.Glu240Lys affected protein folding (PMID:11052664) and resulted in decreased LDL-receptor activity (PMID:1301956).
LDLR-LOVD, British Heart Foundation	RCV000211564	SCV000294938	likely pathogenic	Hypercholesterolemia, familial, 1	2016-03-25	criteria provided, single submitter	literature only
Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix	RCV000211564	SCV000503229	likely benign	Hypercholesterolemia, familial, 1	2016-12-16	criteria provided, single submitter	clinical testing	subject mutated among 2600 FH index cases screened = 1 / previously described in association with FH / Software predictions: Conflicting
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	RCV000211564	SCV000583731	pathogenic	Hypercholesterolemia, familial, 1	2017-03-30	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000586018	SCV000697249	pathogenic	Familial hypercholesterolemia	2016-06-28	criteria provided, single submitter	clinical testing	Variant summary: The LDLR c.718G>A (p.Glu240Lys) variant involves the alteration of a conserved nucleotide and results in a replacement of a medium size and acidic Glutamic acid (E) with a large size and basic Lysine (K) located in the ligand binding domain of LDLR. 3/4 in silico tools predict a damaging outcome for this substitution (SNPs&GO not captured due to low reliability index). This variant was found in 2/121994 control chromosomes at a frequency of 0.0000164, which does not exceed the estimated maximal expected allele frequency of a pathogenic LDLR variant (0.0012508). It was reported in several FH patients indicating its pathogenicity. Additionally a functional study of LDLR function in fibroblast monolayers revealed the variant to only have the WT 15-30% LDL receptor activity suggesting the variant to be a partially transport defective allele that impairs transport between ER and Golgi. Furthermore, the variat was found not to fold into a unique disulphide bond structure like the WT does, thus leading to the conclusion that this variant gives rise to a protein folding defect. Moreover, multiple clinical diagnostic laboratories classified this variant as pathogenic. Taken together, this variant is classified as Pathogenic.
Robarts Research Institute, Western University	RCV000211564	SCV000782952	uncertain significance	Hypercholesterolemia, familial, 1	2018-01-02	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000182341	SCV000888167	pathogenic	not provided	2018-05-22	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000586018	SCV000909146	likely pathogenic	Familial hypercholesterolemia	2023-09-08	criteria provided, single submitter	clinical testing	This missense variant replaces glutamic acid with lysine at codon 240 in LDLR type A repeat 7 of the ligand binding domain of the LDLR protein. This variant is also known as p.Glu219Lys in the mature protein and as FH Charlotte in the literature. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that this variant causes a protein-folding defect (PMID: 10704205, 11052664) and results in partial defect in protein transport between the endoplasmic reticulum and the Golgi apparatus (PMID: 1301956). Cells from a heterozygous carrier individual have shown that this variant causes 15-30% LDLR activity (PMID: 1301956). This variant has been reported in over ten heterozygous individuals affected with familial hypercholesterolemia (PMID: 1301956, 16250003, 23375686, 25463123, 28235710, 24956927, 28965616, 31947532, 32759540, 33303402, 34297352; Laurie et al, 2018, DOI: 10.4172/2327-5790.1000167; Color internal data). This variant has also been observed in compound heterozygous state with another pathogenic truncation variant in at least one individual affected with homozygous familial hypercholesterolemia (PMID: 28965616, 31947532, 32977124). This variant has been identified in 9/282892 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000826173	SCV000967712	likely pathogenic	Homozygous familial hypercholesterolemia	2021-03-22	criteria provided, single submitter	clinical testing	The p.Glu240Lys variant in LDLR (also described as p.Gly219Lys in the literature) has been reported in 8 heterozygous and 3 compound heterozygous individuals with familial hypercholesterolemia (FH) and segregated with disease in 3 affected relatives from two families (Hobbs 1992 PMID: 1301956, Fouchier 2005 PMID: 16250003, Bertolini 2013 PMID: 23375656, Mollaki 2014 PMID: 35463123, Norsworthy 2014 PMID:24956927, Abdul-Husn 2016 PMID:28008010, Pirillo 2017 PMID: 28965616, Xiang 2017 PMID: 28235710, Tada 2018 PMID: 30241732, Trinder 2019 PMID: 31345425). However, this variant has also been reported in one individual with normal cholesterol levels (Abul-Husn 2016 PMID:28008010), suggesting reduced penetrance. This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 200920) and has been identified in 0.005% (7/129192) European chromosomes by gnomAD (http://gnomad.broadinstitute.org/). This frequency is consistent with the frequency of FH in the general population. In vitro functional studies provide some evidence that the p.Glu240Lys variant may impact protein folding and transport of the mature protein from the ER to the Golgi (Hobbs 1992 PMID: 1301956, North 2000 PMID: 11052664, North 2001 PMID: 10704205). Computational prediction tools and conservation analysis do not provide strong support for or against an impact to the protein. In summary, although additional studies are required to fully establish its clinical significance, the p.Glu240Lys variant is likely pathogenic for autosomal dominant FH. The ACMG/AMP Criteria applied: PS4_Moderate; PP1; PM2_Supporting; PM3; PS3_Supporting.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV000211564	SCV001423087	uncertain significance	Hypercholesterolemia, familial, 1	2020-01-22	criteria provided, single submitter	curation	The p.Glu240Lys variant in LDLR has been reported in 7 individuals with Familial Hypercholesterolemia, segregated with disease in 4 affected relatives from 2 families (PMID: 16250003, 25463123, 24956927), and has been identified in 0.005418% (7/129192) of European (non-Finnish) chromosomes, 0.005012% (1/19954) of East Asian chromosomes, and 0.004005% (1/24968) of African chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs768563000). 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, VUS, likely pathogenic variant, and pathogenic variant in ClinVar (Variation ID: 200920). In vitro functional studies with protein imaging provide some evidence that the p.Glu240Lys variant may slightly impact protein folding (PMID: 10704205). 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, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PS3_supporting, PP3, PP1, PS4_Supporting (Richards 2015).
Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	RCV000211564	SCV001432576	pathogenic	Hypercholesterolemia, familial, 1	2018-12-06	criteria provided, single submitter	research
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	RCV000586018	SCV001443701	pathogenic	Familial hypercholesterolemia	2020-04-13	criteria provided, single submitter	clinical testing	This variant, also known as (p.Glu219Lys) or FH Charlotte in the literature, has been previously reported as a heterozygous change in multiple unrelated individuals with Familial Hypercholesterolemia (PMID: 1301956, 16250003, 23375686). Functional studies demonstrate that this variant exhibits reduced receptor activity and impaired protein folding (PMID: 1301956, 11052664, 10704205). It is present in the heterozygous state in the gnomAD population database at a frequency of 0.0032% (9/282892) and thus is presumed to be rare. The c.718G>A (p.Glu240Lys) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.718G>A (p.Glu240Lys) variant is classified as Pathogenic.
Invitae	RCV000586018	SCV001575602	pathogenic	Familial hypercholesterolemia	2023-12-27	criteria provided, single submitter	clinical testing	This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 240 of the LDLR protein (p.Glu240Lys). This variant is present in population databases (rs768563000, gnomAD 0.006%). This missense change has been observed in individuals with clinical features of familial hypercholesterolemia (PMID: 1301956, 16250003, 23375686, 24956927, 25463123, 28235710, 28965616). This variant is also known as E219K. ClinVar contains an entry for this variant (Variation ID: 200920). 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%. Experimental studies have shown that this missense change affects LDLR function (PMID: 11052664). For these reasons, this variant has been classified as Pathogenic.
Laboratory of molecular diagnosis of dyslipidemias, Università egli studi di Napoli Federico II	RCV000211564	SCV001653607	pathogenic	Hypercholesterolemia, familial, 1	2021-05-24	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000211564	SCV002022676	likely pathogenic	Hypercholesterolemia, familial, 1	2022-08-23	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002372113	SCV002673367	likely pathogenic	Cardiovascular phenotype	2023-06-21	criteria provided, single submitter	clinical testing	The p.E240K variant (also known as c.718G>A), located in coding exon 5 of the LDLR gene, results from a G to A substitution at nucleotide position 718. The glutamic acid at codon 240 is replaced by lysine, an amino acid with similar properties. This variant (historically described as p.E219K and FH Charlotte) has been reported in individuals with familial hypercholesterolemia (FH) from a variety of ethnic backgrounds (Hobbs HH et al. Hum. Mutat., 1992;1:445-66; Fouchier SW et al. Hum. Mutat., 2005 Dec;26:550-6; Bertolini S et al. Atherosclerosis, 2013 Apr;227:342-8; Mollaki V et al. Atherosclerosis, 2014 Dec;237:798-804; Xiang R et al. Atherosclerosis, 2017 03;258:84-88). Based on internal structural analysis, this variant is anticipated to disrupt a region of known function (North CL et al. Biochemistry, 2000 Mar;39:2564-71). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Fulgent Genetics, Fulgent Genetics	RCV000211564	SCV002814853	likely pathogenic	Hypercholesterolemia, familial, 1	2021-10-02	criteria provided, single submitter	clinical testing
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	RCV000211564	SCV000606209	pathogenic	Hypercholesterolemia, familial, 1		no assertion criteria provided	research