rs139791325

chr19-11120122-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1 PM2 BP4

The NM_000527.5(LDLR):c.1876G>A(p.Glu626Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000268 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00022 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00027 (0 hom.)
• Consequence: LDLR NM_000527.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:12 B:1 O:1
• Conservation: PhyloP100: 4.79

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM1: In a hotspot region, there are 11 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 11 uncertain in NM_000527.5
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.33752286).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5	c.1876G>A	p.Glu626Lys	missense_variant	13/18	ENST00000558518.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6	c.1876G>A	p.Glu626Lys	missense_variant	13/18	1	NM_000527.5	P3

Frequencies

GnomAD3 genomes AF: 0.000217 AC: 33 AN: 152140 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000328

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000314 AC: 79 AN: 251492 Hom.: 0 AF XY: 0.000324 AC XY: 44 AN XY: 135920

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.000198

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000185

Gnomad NFE exome AF: 0.000615

Gnomad OTH exome AF: 0.000489

GnomAD4 exome AF: 0.000274 AC: 400 AN: 1461818 Hom.: 0 Cov.: 33 AF XY: 0.000263 AC XY: 191 AN XY: 727210

Gnomad4 AFR exome AF: 0.0000597

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.000153

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000300

Gnomad4 NFE exome AF: 0.000312

Gnomad4 OTH exome AF: 0.000480

GnomAD4 genome AF: 0.000217 AC: 33 AN: 152140 Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18 AN XY: 74320

Gnomad4 AFR AF: 0.0000483

Gnomad4 AMR AF: 0.000328

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.000309

Gnomad4 OTH AF: 0.000478

Alfa AF: 0.000289 Hom.: 0

Bravo AF: 0.000174

TwinsUK AF: 0.000539 AC: 2

ALSPAC AF: 0.00 AC: 0

ExAC AF: 0.000486 AC: 59

EpiCase AF: 0.00

EpiControl AF: 0.000652

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:12 Benign:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:2 Uncertain:5 Benign:1

Pathogenic, criteria provided, single submitter	clinical testing	U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	Jan 31, 2024	This missense variant LDLR:c.1876G>A (also known as p.Glu605Lys in the mature protein), replaces a glutamic acid with lysine at codon 626 of the LDLR protein (p.Glu626Lys). According to updated genomic data and to ClinGen FH VCEP criteria issued in 2022 (PMID: 34906454) for the validation of pathogenicity of LDLR variants, this variant may now be classified as “Pathogenic" with low penetrance from evidence as follows. It is located within a highly conserved motif of a functional domain (LDLR Class B6) essential for LDL binding and LDLR recycling to the plasma membrane. Despite being previously classified as VUS according to standard ACMG criteria and found as VUS in multiple records in ClinVar, recent in-vitro studies (PMID: 35568682) have reclassified this variant as “Pathogenic” based on level 1 functional tests showing significantly reduced LDL binding and internalization (PS3-strong) and cosegregation found with FH in at least 6 informative meioses (PP1-Strong). In addition, this variant was observed in the context of genetic testing in a patient exhibiting a phenotype (Dutch Lipid Clinic Network Scoring=11) of definite FH (PP4), and is now borderline to meeting criteria PM2 (GnomAD= 0.000217 (<0.0002) and no homozygotes) and PP3 (REVEL Score= 0,71, ≥0,75). Studies mentioning this variant as likely benign performed as part of screening studies before 2013, and discordant observations suggesting VUS in previous CLinGen reports, are in favor of a lowered penetrance for this variant. -
Uncertain significance, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	Jul 30, 2015	- -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Feb 05, 2024	This missense variant replaces glutamic acid with lysine at codon 626 of the LDLR protein. This variant is also known as p.Glu605Lys in the mature protein. This variant alters a conserved glutamic acid residue in the LDLR type B repeat 6 of the LDLR protein (a.a. 616-658), where pathogenic missense variants are found enriched (ClinVar-LDLR). Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. Functional studies have shown that this variant causes a decrease in LDLR internalization, uptake and activity (PMID: 35568682, 37719435); a different high-throughput cell-based assay was inconclusive regarding the impact of this variant on the LDLR function (PMID: 25647241). This variant has been reported in several individuals affected with familial hypercholesterolemia (PMID: 16250003, 20828696, 27596133, 35474963, 37848354). Two of these individuals also carried a different pathogenic LDLR missense variant (PMID: 27596133). In a large myocardial infarction case-control study conducted in Europe and North America, this variant was reported in 4/3726 cases and 3/3668 controls, showing inconclusive association with disease (PMID: 25487149). This variant has been identified in 83/282896 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. -
Pathogenic, no assertion criteria provided	clinical testing	Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital	May 25, 2011	- -
Uncertain significance, criteria provided, single submitter	research	Laboratory of Genetics and Molecular Cardiology, University of São Paulo	Mar 01, 2016	- -
Uncertain significance, criteria provided, single submitter	research	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	Mar 01, 2016	0/200 non-FH alleles -
Likely benign, flagged submission	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Feb 19, 2019	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

not specified Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Feb 03, 2017	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: This variant is present in HGMD in 3 papers but in cases and controls. It is classified in ClinVar with 1 star as Likely benign by British Heart Foundation, VUS by CHOP and Instituto Nacional de Saude Doutor Ricardo Jorge and Pathogenic by PathWest Laboratory Medicine WA - Fiona Stanley Hospital (in 2011). It has a max MAF in ExAC of 0.08% (56 alleles) and in gnomAD of 0.06% (75 alleles). -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 14, 2022	Variant summary: LDLR c.1876G>A (p.Glu626Lys) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00032 in 253384 control chromosomes (gnomAD and Do_2015), predominantly at a frequency of 0.00062 within the Non-Finnish European subpopulation in the gnomAD database. This frequency is not significantly higher than expected for a pathogenic variant in LDLR causing Familial Hypercholesterolemia (0.00032 vs 0.0013), allowing no conclusion about variant significance. c.1876G>A has been reported in the literature in individuals affected with Familial Hypercholesterolemia and has been reported to segregate within disease, however it has also been reported in the compound heterozygous state in individuals with a pathogenic variant (e.g. Fouchier_2005, Medeiros_2014, Thormaehlen_2015, Benito-Vicente_2015, Do_2015, Grenkowitz_2016,Futema_2021, Graca_2022). These reports do not provide unequivocal conclusions about association of the variant with Familial Hypercholesterolemia. At least two publications report experimental evidence evaluating an impact on protein function, however the results indicate the effect is unclear (e.g. Thormaehlen_2015, Graca_2022). The variant was found to have normal expression and ligand binding levels, but showed reduced cellular internalization, approximately 60% of the WT protein, suggesting it may impact function (Graca_2022). Eleven submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments. The majority classified the variant as VUS (n=9), one classified it as likely pathogenic, and one as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance. -

Familial hypercholesterolemia Uncertain:3

Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 07, 2023	This missense variant replaces glutamic acid with lysine at codon 626 of the LDLR protein. This variant is also known as p.Glu605Lys in the mature protein. This variant alters a conserved glutamic acid residue in the LDLR type B repeat 6 of the LDLR protein (a.a. 616-658), where pathogenic missense variants are found enriched (ClinVar-LDLR). Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. Functional studies have shown that this variant causes a decrease in LDLR internalization, uptake and activity (PMID: 35568682, 37719435); a different high-throughput cell-based assay was inconclusive regarding the impact of this variant on the LDLR function (PMID: 25647241). This variant has been reported in several individuals affected with familial hypercholesterolemia (PMID: 16250003, 20828696, 27596133, 35474963, 37848354). Two of these individuals also carried a different pathogenic LDLR missense variant (PMID: 27596133). In a large myocardial infarction case-control study conducted in Europe and North America, this variant was reported in 4/3726 cases and 3/3668 controls, showing inconclusive association with disease (PMID: 25487149). This variant has been identified in 83/282896 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Oct 03, 2022	This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 626 of the LDLR protein (p.Glu626Lys). This variant is present in population databases (rs139791325, gnomAD 0.06%). This missense change has been observed in individual(s) with hypercholesterolemia and myocardial infarction (PMID: 16250003, 20828696, 25487149, 25647241). ClinVar contains an entry for this variant (Variation ID: 183127). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on LDLR protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 06, 2021

The p.E626K variant (also known as c.1876G>A), located in coding exon 13 of the LDLR gene, results from a G to A substitution at nucleotide position 1876. The glutamic acid at codon 626 is replaced by lysine, an amino acid with similar properties. This variant has been reported in family hypercholesterolemia (FH), myocardial infarction, and coronary artery disease cohorts; however, it has also been reported in individuals with normal LDL-C levels (Fouchier SW et al. Hum Mutat, 2005 Dec;26:550-6; Medeiros AM et al. J Lipid Res, 2014 May;55:947-55; Thormaehlen AS et al. PLoS Genet, 2015 Feb;11:e1004855; Do R et al. Nature, 2015 Feb;518:102-6; Grenkowitz T et al. Atherosclerosis, 2016 10;253:88-93; Benedek P et al. J Intern Med, 2018 12;284:674-684). Based on data from gnomAD, the frequency for this variant is above the maximum credible frequency for a disease-causing variant in this gene based on internally established thresholds (Karczewski et al. Nature. 2020 May;581(7809):434-443; Whiffin et al. Genet Med. 2017 10;19:1151-1158). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -

not provided Other:1

not provided, no classification provided

in vitro

Dept. of Genetics and Pharmacogenomics, Merck Research Labs

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Uncertain	0.097	D
BayesDel_noAF	Pathogenic	0.27
Cadd	Uncertain	25
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.83	D;.;.;.;.;.
Eigen	Benign	-0.18
Eigen_PC	Benign	-0.12
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.97	D;D;D;D;D;D
M_CAP	Pathogenic	0.46	D
MetaRNN	Benign	0.34	T;T;T;T;T;T
MetaSVM	Uncertain	0.28	D
MutationAssessor	Benign	1.2	L;.;.;.;.;L
MutationTaster	Benign	0.87	D;D;D;D;D;D;D
PrimateAI	Uncertain	0.55	T
PROVEAN	Uncertain	-3.2	D;D;D;D;D;D
Sift	Benign	0.055	T;T;T;D;T;T
Sift4G	Benign	0.092	T;T;T;T;T;T
Polyphen		0.64	P;.;.;.;.;.
Vest4		0.68
MVP		1.0
MPC		0.41
ClinPred		0.11	T
GERP RS		4.3
Varity_R		0.60
gMVP		0.98

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		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

Other links and lift over

dbSNP: rs139791325; hg19: chr19-11230798;