rs768563000

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1PM2PP3_ModeratePP5_Very_Strong

The NM_000527.5(LDLR):c.718G>A(p.Glu240Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Synonymous variant affecting the same amino acid position (i.e. E240E) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000040 ( 0 hom. )

Consequence

LDLR
NM_000527.5 missense

Scores

Clinical Significance

Pathogenic reviewed by expert panel P:17U:2B:1

Conservation

PhyloP100: 2.19

Variant links:

Genes affected

LDLR (HGNC:6547): (low density lipoprotein receptor) The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. The encoded protein is normally bound at the cell membrane, where it binds low density lipoprotein/cholesterol and is taken into the cell. Lysosomes release the cholesterol, which is made available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the rate-limiting step in cholesterol synthesis. At the same time, a reciprocal stimulation of cholesterol ester synthesis takes place. Mutations in this gene cause the autosomal dominant disorder, familial hypercholesterolemia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2022]

LDLR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 14 ACMG points.

PM1

In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 8 uncertain in NM_000527.5

PM2

Very rare variant in population databases, with high coverage;

PP3

MetaRNN computational evidence supports a deleterious effect, 0.938

PP5

Variant 19-11106588-G-A is Pathogenic according to our data. Variant chr19-11106588-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 200920.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr19-11106588-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5 linkuse as main transcript	c.718G>A	p.Glu240Lys	missense_variant	5/18	ENST00000558518.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6 linkuse as main transcript	c.718G>A	p.Glu240Lys	missense_variant	5/18	1	NM_000527.5	P3	P01130-1

Frequencies

GnomAD3 genomes

AF:

0.0000328

AC:

AN:

152212

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000588

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000278

AC:

AN:

251486

Hom.:

AF XY:

0.0000221

AC XY:

AN XY:

135922

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000527

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000404

AC:

AN:

1461868

Hom.:

Cov.:

AF XY:

0.0000344

AC XY:

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000504

Gnomad4 OTH exome

AF:

0.0000166

GnomAD4 genome

AF:

0.0000328

AC:

AN:

152212

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.0000241

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000588

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000134

Hom.:

Bravo

AF:

0.0000264

ExAC

AF:

0.0000165

AC:

EpiCase

AF:

0.0000545

EpiControl

AF:

0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:17Uncertain:2Benign:1

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Hypercholesterolemia, familial, 1

Pathogenic:9Uncertain:2Benign:1

Likely pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Robarts Research Institute, Western University	Jan 02, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital	Jan 05, 2022	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). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Aug 23, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	Mar 30, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory of molecular diagnosis of dyslipidemias, Università egli studi di Napoli Federico II	May 24, 2021	- -
Uncertain significance, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 22, 2020	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). -
Pathogenic, criteria provided, single submitter	research	Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	Dec 06, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 02, 2021	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	Feb 14, 2022	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. -
Pathogenic, no assertion criteria provided	research	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix	Dec 16, 2016	subject mutated among 2600 FH index cases screened = 1 / previously described in association with FH / Software predictions: Conflicting -

Familial hypercholesterolemia

Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 27, 2023	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	Apr 13, 2020	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 28, 2016	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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Sep 08, 2023	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. -

not provided

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 22, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 12, 2022	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) -

Homozygous familial hypercholesterolemia

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 22, 2021

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. -

Cardiovascular phenotype

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 12, 2024

The c.718G>A (p.E240K) alteration is located in exon 5 (coding exon 5) of the LDLR gene. This alteration results from a G to A substitution at nucleotide position 718, causing the glutamic acid (E) at amino acid position 240 to be replaced by a lysine (K). Based on data from gnomAD, the A allele has an overall frequency of 0.003% (9/282892) total alleles studied. The highest observed frequency was 0.005% (7/129192) of European (non-Finnish) alleles. 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, 1992; Fouchier, 2005; Bertolini, 2013; Mollaki, 2014; Xiang, 2017). This amino acid position is well conserved in available vertebrate species. Based on internal structural analysis, this variant is anticipated to disrupt a region of known function (North, 2000). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.48

BayesDel_addAF

Pathogenic

0.35

BayesDel_noAF

Pathogenic

0.43

Cadd

Uncertain

Dann

Pathogenic

1.0

DEOGEN2

Pathogenic

0.82

D;.;.;.;.

Eigen

Uncertain

0.30

Eigen_PC

Uncertain

0.27

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.94

D;D;D;D;D

M_CAP

Pathogenic

0.82

MetaRNN

Pathogenic

0.94

D;D;D;D;D

MetaSVM

Pathogenic

0.99

MutationAssessor

Benign

1.7

L;.;.;.;L

MutationTaster

Benign

1.0

D;D;D;D;D;D;D

PrimateAI

Uncertain

0.53

PROVEAN

Uncertain

-2.7

D;D;D;N;D

Sift

Uncertain

0.0040

D;D;D;T;D

Sift4G

Uncertain

0.0060

D;D;D;D;D

Polyphen

0.97

D;.;.;.;.

Vest4

0.79

MutPred

0.76

Gain of methylation at E240 (P = 0.0017);Gain of methylation at E240 (P = 0.0017);.;.;Gain of methylation at E240 (P = 0.0017);

MVP

1.0

MPC

0.84

ClinPred

0.64

GERP RS

4.0

Varity_R

0.89

gMVP

0.91

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over