rs5928

chr19-11129564-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Moderate BP6 BS2

The NM_000527.5(LDLR):c.2441G>A(p.Arg814Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000214 in 1,613,850 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R814W) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0011 (2 hom., cov: 31)
  • Exomes 𝑓: 0.00012 (0 hom.)
• Consequence: LDLR NM_000527.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:6 B:8 O:1
• Conservation: PhyloP100: 4.12

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 Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.08873907).
• BP6: Variant 19-11129564-G-A is Benign according to our data. Variant chr19-11129564-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 161278.We mark this variant Likely_benign, oryginal submissions are: {Benign=3, Likely_benign=5, Likely_pathogenic=1, Uncertain_significance=4, not_provided=1}. Variant chr19-11129564-G-A is described in Lovd as [Likely_benign].
• BS2: High Homozygotes in GnomAd at 2 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5	c.2441G>A	p.Arg814Gln	missense_variant	17/18	ENST00000558518.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6	c.2441G>A	p.Arg814Gln	missense_variant	17/18	1	NM_000527.5	P3

Frequencies

GnomAD3 genomes AF: 0.00111 AC: 168 AN: 151912 Hom.: 2 Cov.: 31

Gnomad AFR AF: 0.00384

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000526

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: 0.0000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000259 AC: 65 AN: 251446 Hom.: 0 AF XY: 0.000162 AC XY: 22 AN XY: 135904

Gnomad AFR exome AF: 0.00351

Gnomad AMR exome AF: 0.000116

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000176

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000121 AC: 177 AN: 1461820 Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 88 AN XY: 727214

Gnomad4 AFR exome AF: 0.00412

Gnomad4 AMR exome AF: 0.000179

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000719

Gnomad4 OTH exome AF: 0.000364

GnomAD4 genome AF: 0.00111 AC: 169 AN: 152030 Hom.: 2 Cov.: 31 AF XY: 0.00104 AC XY: 77 AN XY: 74312

Gnomad4 AFR AF: 0.00386

Gnomad4 AMR AF: 0.000525

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000242 Hom.: 0

Bravo AF: 0.00142

ESP6500AA AF: 0.00295 AC: 13

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000280 AC: 34

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:6 Benign:8 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

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

Likely benign, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Uncertain significance, criteria provided, single submitter	research	Laboratory of Genetics and Molecular Cardiology, University of São Paulo	Mar 01, 2016	- -
Likely 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.2441G>A (also known as p.Arg793Gln in the mature protein), replaces an arginine with glutamine at codon 814 of the LDLR protein (p.Arg814Gln). 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 “Likely Pathogenic” from evidence as follows. It is located within a highly conserved functional domain (Cytoplasmic domain) essential for LDLR internalization. This variant was historically assessed in-vivo (PM3) and in-vitro in homozygous FH (PS3-moderate), observed as a founder mutation for FH (PS4) or a polymorphism at risk of hypercholesterolemia in populations of African ancestry, and was estimated as pathogenic in-silico (REVEL= 0,768) by disrupting a domain required for MYLIP-triggered down-regulation of LDLR (PP3). However, discrepant observations in mildly hypercholesterolemic or normolipidemic subjects, a high frequency in the general population (GnomAD= 0.00111, with no homozygotes) and lack of high-level in-vitro functional studies lead to classify this variant as “Likely Pathogenic” with low penetrance. -
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	subjects mutated among 2600 FH index cases screened = 3 , family member = 1/previously described in association with FH/Software predictions: Conflicting -
Uncertain significance, criteria provided, single submitter	clinical testing	New York Genome Center	Jul 02, 2021	The c.2441G>A (p.Arg814Gln) variant identified in the LDLR gene substitutes a moderately conserved Arginine for Glutamine at amino acid 814/861(exon 17/18). This variant is found with appreciable frequency in gnomAD(v3.1.1), including in two homozygotes (168 heterozygotes, 2 homozygotes; allele frequency:1.11e-3), which is higher than expected for a pathogenic variant in the LDLR gene. The c.2441G>A (p.Arg814Gln) variant is reported in ClinVar as Pathogenic, Likely Pathogenic, Likely Benign, and as a Variant of Uncertain Significance (VarID:161278). This variant has been identified in many affected individuals in the literature, although its role in relation to hyperlipidemia in those individuals is not clearly defined [PMID:9544746, 10882754, 16389549, 27784735, 33508743]. In silico algorithms predict this variant to be Damaging (SIFT; score:0.00) and Pathogenic (REVEL; score:0.768) to the function of the canonical transcript. While the c.2441G>A(p.Arg814Gln) variant identified in the LDLR gene has been identified in many affected individuals in the literature and is predicted damaging by in silico predictors, its allele frequency is higher than expected. Given the conflicting evidence regarding its pathogenicity, the c.2441G>A (p.Arg814Gln) variant identified in the LDLR gene is reported as a Variant of Uncertain Significance. -

not provided Uncertain:3 Benign:1 Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Mar 14, 2022	Identified in individuals with confirmed or suspected familial hypercholesterolemia (FH) (Arca et al., 1998; Vergotine et al., 2001; Fouchier et al., 2005; Humphries et al., 2006; Lange et al., 2014; Santos et al., 2014; Sanchez-Hernandez et al., 2016; Martin-Campos et al., 2018; Futema et al., 2021), familial combined hyperlipidemia (Minicocci et al., 2015), coronary heart disease (Thiart et al., 2000), and/or a history of early myocardial infarction (Do et al., 2015); In silico analysis supports that this missense variant does not alter protein structure/function; Published functional studies demonstrate conflicting results with some studies showing significantly lower fractional catabolic rate which suggests reduced in vivo LDL receptor activity (Arca et al., 1998), while other studies show LDL uptake is similar to wild type suggesting no functional impact (Thormaehlen et al., 2015); Also known as R793Q; This variant is associated with the following publications: (PMID: 26332594, 35047021, 24055113, 25637381, 25487149, 10882754, 24507775, 16250003, 16389549, 24529145, 25647241, 32906206, 11845603, 26342331, 27784735, 30293936, 33508743, 9544746, 32719484) -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2022	LDLR: BS1, BS2 -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The LDLR p.Arg646Gln variant was identified in 4 of 1430 proband chromosomes (frequency: 0.0028) from individuals or families with familial hypercholesterolemia (FH) or high LDL-C (Humphries_2006_PMID:16389549; Thiart_2000_PMID:10882754; Santos_2014_PMID:24529145; Lange_2014_PMID:24507775). The variant was also identified in dbSNP (ID: rs5928), LOVD 3.0 and ClinVar (classified as likely benign by 4 submitters, as a VUS by 3 submitters, as likely pathogenic by 1 submitter and as pathogenic by 1 submitter). The variant was identified in control databases in 101 of 282836 chromosomes at a frequency of 0.000357 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 93 of 24970 chromosomes (freq: 0.003724), Other in 1 of 7224 chromosomes (freq: 0.000138), Latino in 4 of 35440 chromosomes (freq: 0.000113), South Asian in 1 of 30614 chromosomes (freq: 0.000033) and European (non-Finnish) in 2 of 129174 chromosomes (freq: 0.000015), while the variant was not observed in the Ashkenazi Jewish, East Asian or European (Finnish) populations. The p.Arg646 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Sep 21, 2023	In the published literature, this variant has been reported in several individuals affected with hypercholesterolemia (PMIDs: 10882754 (2000), 11845603 (2001), 16250003 (2005), 16389549 (2006), 24529145 (2014), 26802169 (2016), 28220743 (2017), 30293936 (2018), 34040191 (2021), 35047021 (2021), 36769678 (2023)). In addition, this variant was also reported to occur with other variants in affected individuals (PMIDs: 27784735 (2016), 34496902 (2021)). Functional studies of this variant reported reduced LDLR degradation (PMID: 9544746 (1998)) and that the variant did not disrupt LDL uptake activity (PMID: 25647241 (2015)), however, further research is needed. The frequency of this variant in the general population, 0.0037 (93/24970 chromosomes in African/African American subpopulation (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is higher than would generally be expected for pathogenic variants in this gene. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. -
not provided, no classification provided	in vitro	Dept. of Genetics and Pharmacogenomics, Merck Research Labs	-	- -

not specified Benign:2

Benign, criteria provided, single submitter	clinical testing	Mendelics	Aug 22, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 07, 2023	Variant summary: LDLR c.2441G>A (p.Arg814Gln) results in a conservative amino acid change in 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 0.00036 in 282994 control chromosomes, predominantly at a frequency of 0.0037 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 3.7 fold of the estimated maximal expected allele frequency for a pathogenic variant in LDLR causing Early Onset Coronary Artery Disease phenotype (0.001), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. c.2441G>A has been reported in the literature in individuals affected with hypercholesterolemia without strong evidence for causality (e.g. Arca_1997, Thiart_2000, Vergotine_2001, Humphries_2006, Sanchez-Hernandez_2016, Futema_2021, DErasmo_2021, Rimbert_2022). These reports do not provide unequivocal conclusions about association of the variant with Early Onset Coronary Artery Disease. One co-occurrence with another pathogenic variants has been reported (LDLR c.2389G>A, p.Val797Met), providing supporting evidence for a benign role. At least one publication reports a modest reduction of LDL-R activity in-vivo in a patient with the variant (e.g. Arca_1997). Twelve ClinVar submitters (evaluation after 2014) cite this variant as benign (n=2), likely benign (n=4), uncertain significance (n=5) and likely pathogenic (n=1). Multiple laboratories reported the variant with conflicting assessments. Based on the evidence outlined above, the variant was classified as likely benign. -

Familial hypercholesterolemia Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 23, 2020	- -
Likely benign, criteria provided, single submitter	clinical testing	Invitae	Jan 27, 2024	- -

Hypercholesterolemia Uncertain:1

Uncertain significance, no assertion criteria provided

research

CSER _CC_NCGL, University of Washington

Jun 01, 2014

- -

Cardiovascular phenotype Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 19, 2022

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.036	T
BayesDel_noAF	Pathogenic	0.24
Cadd	Uncertain	25
Dann	Uncertain	1.0
Eigen	Uncertain	0.36
Eigen_PC	Uncertain	0.38
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Benign	0.33	T
M_CAP	Pathogenic	0.74	D
MetaRNN	Benign	0.089	T
MutationTaster	Benign	1.0	D;D;D;D;D;D;N
PROVEAN	Benign	1.1	N
Sift	Pathogenic	0.0	D
Sift4G	Benign	0.17	T
Vest4		0.79
MVP		1.0
ClinPred		0.027	T
GERP RS		4.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs5928; hg19: chr19-11240240;