19-11120478-C-T

Position:

chr19-11120478-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 5P and 4B. PP1_StrongBS4PP3

This summary comes from the ClinGen Evidence Repository: NM_000527.5(LDLR):c.2096C>T (p.Pro699Leu) variant is classified as Uncertain significance for Familial Hypercholesterolemia by applying evidence codes (BS4, PP1_Strong and PP3) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1101/2021.03.17.21252755). The supporting evidence is as follows: BS4 - Variant does not segregate with FH phenotype in 11 informative meioses in 6 families (Laboratory of Genetics and Molecular Cardiology).PP1_strong - Variant segregates with FH phenotype in 58 informative meioses in 9 families from Laboratory of Genetics and Molecular Cardiology.PP3 - REVEL: 0,92. LINK:https://erepo.genome.network/evrepo/ui/classification/CA038525/MONDO:0007750/013

Frequency

Genomes: 𝑓 0.000092 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000014 ( 0 hom. )

Consequence

LDLR
NM_000527.5 missense

Scores

Clinical Significance

Uncertain significance reviewed by expert panel P:17U:4

Conservation

PhyloP100: 7.89

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 Uncertain_significance. Variant got 1 ACMG points.

PP1

PP3

BS4

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5 linkuse as main transcript	c.2096C>T	p.Pro699Leu	missense_variant	14/18	ENST00000558518.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6 linkuse as main transcript	c.2096C>T	p.Pro699Leu	missense_variant	14/18	1	NM_000527.5	P3	P01130-1

Frequencies

GnomAD3 genomes

AF:

0.0000920

AC:

AN:

152140

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000338

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000199

AC:

AN:

251028

Hom.:

AF XY:

0.0000221

AC XY:

AN XY:

135732

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.0000289

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:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000137

AC:

AN:

1461566

Hom.:

Cov.:

AF XY:

0.0000179

AC XY:

AN XY:

727106

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.0000224

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000464

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000629

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000920

AC:

AN:

152140

Hom.:

Cov.:

AF XY:

0.0000942

AC XY:

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.000338

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:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000273

Hom.:

Bravo

AF:

0.0000869

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.0000165

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:17Uncertain:4

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Hypercholesterolemia, familial, 1

Pathogenic:8Uncertain:4

Likely pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Oct 31, 2019	The c.2096C>T (p.Pro699Leu) variant in exon 14 of LDLR gene results in an amino acid change at residue 699 from a proline to a leucine. This variant has been reported in multiple unrelated individuals and families with familial hypercholesterolemia (PMID: 21642693, 7489239, 21310417, 26892515, 25461735, 10882754). Multiple lines of in silico algorithms have predicted this p.Pro699Leu change to be deleterious. Functional studies (PMID: 20089850) demonstrated that the mutant protein misfolded with a loss of normal protein tracking pattern. Therefore, this variant c.2096C>T (p.Pro699Leu) of LDLR is classified as likely pathogenic. -
Likely pathogenic, 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	- -
Pathogenic, criteria provided, single submitter	clinical testing	Division of Medical Genetics, University of Washington	Sep 10, 2019	This variant has an overall allele frequency of 0.00004 in the Broad Institute gnomAD Browser (https://gnomad.broadinstitute.org/). In silico analyses indicate this is an evolutionarily conserved residue. This variant has been reported in the literature in multiple individuals and families with familial hypercholesterolemia (Schuster 1995, Thiart 2000, Fouchier 2001, Van Gaal 2001, Huijgen 2011, Tichy 2012, Bertolini 2013, Janness 2015, Sharifi 2016, Wang 2016). Thus, this variant is interpreted as pathogenic. -
Uncertain significance, reviewed by expert panel	curation	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	Jun 18, 2021	NM_000527.5(LDLR):c.2096C>T (p.Pro699Leu) variant is classified as Uncertain significance for Familial Hypercholesterolemia by applying evidence codes (BS4, PP1_Strong and PP3) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1101/2021.03.17.21252755). The supporting evidence is as follows: BS4 - Variant does not segregate with FH phenotype in 11 informative meioses in 6 families (Laboratory of Genetics and Molecular Cardiology). PP1_strong - Variant segregates with FH phenotype in 58 informative meioses in 9 families from Laboratory of Genetics and Molecular Cardiology. PP3 - REVEL: 0,92. -
Pathogenic, criteria provided, single submitter	clinical testing	U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	Mar 30, 2017	- -
Likely pathogenic, 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 , family members = 3 with co-segregation / previously described in association with FH/software prediction damaging -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	May 27, 2022	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation	Nov 05, 2016	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Robarts Research Institute, Western University	-	- -
Pathogenic, no assertion criteria provided	research	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	-	- -
Uncertain significance, criteria provided, single submitter	research	Fundacion Hipercolesterolemia Familiar	Mar 01, 2016	- -

not provided

Pathogenic:4

Likely pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Apr 21, 2023	BS4, PP1, PP3, PM3, PS4 -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 18, 2023	Located in the third EGF-like repeat within the LDL-receptor EGF precursor homology domain (Sudhof et al., 1985; Rudenko et al., 2002); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(P678L); This variant is associated with the following publications: (PMID: 11810272, 21310417, 26892515, 10882754, 19318025, 23375686, 22390909, 11851376, 7489239, 24507775, 21642693, 25461735, 22698793, 31447099, 34456049, 35480308, 20089850, 34040191, 32719484, 34037665, 33740630, 33303402, 30586733, 32041611, 31106297, 35339733, 32220565, 23064986, 27824480, 34234266, 27765764, 33994402) -
Likely pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Sep 29, 2023	The LDLR c.2096C>T p.Pro699Leu variant, also known as Pro678Leu, (rs201573863) is reported in the literature in several individuals and families with clinically diagnosed familial hypercholesterolemia (selected publications: Ajufo 2021, Brown 2020, Lange 2014, Sun 2018), including a few homozygous or compound heterozygous individuals affected with severe disease (Santos 2014, Schuster 1995). This variant is also reported in ClinVar (Variation ID: 252219), and is found in the general population with an overall allele frequency of 0.0034% (11/282422 alleles) in the Genome Aggregation Database. Computational analyses predict that this variant is deleterious (REVEL: 0.920). Based on available information, this variant is considered to be likely pathogenic. References: Ajufo E et al. A randomized controlled trial of genetic testing and cascade screening in familial hypercholesterolemia. Genet Med. 2021 Sep;23(9):1697-1704. PMID: 34040191. Brown EE et al. Incorporation of genetic testing significantly increases the number of individuals diagnosed with familial hypercholesterolemia. J Clin Lipidol. 2020 May-Jun;14(3):331-338. PMID: 32220565. Lange LA et al. Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. Am J Hum Genet. 2014 Feb 6;94(2):233-45. PMID: 24507775. Santos RD. What are we able to achieve today for our patients with homozygous familial hypercholesterolaemia, and what are the unmet needs? Atheroscler Suppl. 2014 Sep;15(2):19-25. PMID: 25257073. Schuster H et al. Ten LDL receptor mutants explain one third of familial hypercholesterolemia in a German sample. Arterioscler Thromb Vasc Biol. 1995 Dec;15(12):2176-80. PMID: 7489239. Sun YV et al. Effects of Genetic Variants Associated with Familial Hypercholesterolemia on Low-Density Lipoprotein-Cholesterol Levels and Cardiovascular Outcomes in the Million Veteran Program. Circ Genom Precis Med. 2018 Dec;11(12):e002192. PMID: 31106297. -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Nov 21, 2019	The best available variant frequency is uninformative because it is below the disease allele frequency. Predicted to have a damaging effect on the protein. In multiple individuals, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic. This variant is statistically more frequent in affected individuals than in the general population and/or healthy controls. -

Familial hypercholesterolemia

Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Sep 21, 2023	Variant summary: LDLR c.2096C>T (p.Pro699Leu) results in a non-conservative amino acid change located in the EGF-like domain (IPR000742) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2e-05 in 251028 control chromosomes. c.2096C>T has been reported in the literature as a heterozygous genotype in multiple individuals affected with autosomal dominant Familial Hypercholesterolemia (example, Schuster_1995, Huijgen_2012, Bertolini_2013, Jannes_2015, Wang_2016, Tichy_2012, Ahmad_2012, Marco-Benedi_2022, Sharifi_2016) to include at-least one compound heterozygous proband with severe Hypercholesterolemia whose obligate carrier father with this variant was reportedly unaffected, i.e., normal cholesterol levels at age 39 (Schuster_1995). This same study also reported co-segregation with Hypercholesterolemia in a second family but did not provide primary evidence supporting this finding (Schuster_1995). As the variant allele was transmitted much more often than the reference allele to affected members in tested families, these data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 23064986, 23375686, 22698793, 22390909, 25461735, Wang_2016 has NO_PMID, 7489239, 34456049, 26892515). Multiple submitters including an expert panel (ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel) have cited clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments but a predominant consensus as Pathogenic/Likely pathogenic (n=12) and VUS (n=4 to include the Expert Panel). Some submitters cite overlapping evidence utilized in the context of this evaluation while the Expert Panel cites both apparent non-segregation and co-segregation without providing primary evidence for independent corroboration. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 24, 2024	This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 699 of the LDLR protein (p.Pro699Leu). This variant is present in population databases (rs201573863, gnomAD 0.04%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 7489239, 10882754, 21310417, 21642693, 22390909, 23375686, 25461735, 26892515, 27765764). This variant is also known as Pro678Leu. ClinVar contains an entry for this variant (Variation ID: 252219). 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%. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 03, 2023	This missense variant replaces proline with leucine at codon 699 in the EGF-like repeat C of the EGF precursor homology domain of the LDLR protein. This variant is also known as p.Pro678Leu in the mature protein. 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). A functional study using transfected HeLa cells has shown that this variant causes LDLR protein misfolding and retention in the endoplasmic reticulum (PMID: 20089850). This variant has been reported in over 20 individuals affected with familial hypercholesterolemia (PMID: 10882754, 11810272, 11851376, 19318025, 21310417, 21642693, 22698793, 23064986, 23375686, 26892515, 27824480, 33994402, 34037665, 35137788). While this variant has been shown to segregate with disease, with 58 informative meioses across 9 families, it has also shown non-segregation in 11 informative meioses across 6 families (ClinVar SCV001960938.1). This variant has been identified in 11/282422 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Homozygous familial hypercholesterolemia

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 26, 2019

The p.Pro699Leu variant in LDLR (also reported as p.Pro678Leu in the literature) has been reported in the heterozygous state at least 11 individuals with familial hypercholesterolemia (FH) and 7 individuals with suspected FH (Thiart 2000, Fouchier 2001, Van Gaal 2001, Huijgen 2011, Tichy 2012, Bertolini 2013, Jannes 2015, Wang 2016, Sharif 2016). It was also identified in 1 individual with homozygous FH who had a second pathogenic loss of function variant in LDLR (Schuster 1995). This variant was also present in this individual's father who had normal cholesterol levels, suggesting reduced penetrance. The p.Pro699Leu variant has been reported by other clinical laboratories in ClinVar (Variation ID# 252219) and has been identified in 9/24032 African chromosomes by the Genome Aggregation Database (GnomAD, http://gnomad.broadinstitute.org; dbSNP rs201573863). This frequency is low enough to be consistent with the frequency of FH in the general population. Computational prediction tools and conservation analysis suggest that the p.Pro699Leu variant may impact the protein. In summary, although additional studies are required to fully establish its clinical significance, the p.Pro699Leu variant is likely pathogenic. The ACMG/AMP Criteria applied (Richards 2015): PS4, PM2_supporting, PP3. -

Cardiovascular phenotype

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 27, 2024

The p.P699L variant (also known as c.2096C>T), located in coding exon 14 of the LDLR gene, results from a C to T substitution at nucleotide position 2096. The proline at codon 699 is replaced by leucine, an amino acid with similar properties. This variant, also known as p.P678L, has been reported in numerous familial hypercholesterolemia (FH) cohorts, though clinical details were limited in many of the studies (e.g., Thiart R et al. J. Med. Genet., 2000 Jul;37:514-9; Ahmad Z et al, Circ Cardiovasc Genet 2012 Dec; 5(6):666-75; Sharifi M et al. Metab. Clin. Exp., 2016 Mar;65:48-53; Jannes CE et al. Atherosclerosis, 2015 Jan;238:101-7; Wang J et al. Arterioscler. Thromb. Vasc. Biol., 2016 12;36:2439-2445; Gabová D et al. Physiol Res, 2017 Mar;66:75-84; Kawame H et al. J Hum Genet, 2021 Jul;). This alteration has also been described in the compound heterozygous or homozygous state in multiple probands with homozygous FH (Schuster H et al, Arterioscler. Thromb. Vasc. Biol. 1995 Dec; 15(12):2176-80; Santos RD. Atheroscler Suppl, 2014 Sep;15:19-25). This amino acid position is highly 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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.71

BayesDel_addAF

Pathogenic

0.33

BayesDel_noAF

Pathogenic

0.59

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Pathogenic

0.95

D;.;.;.;.

Eigen

Pathogenic

0.84

Eigen_PC

Pathogenic

0.70

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Pathogenic

1.0

D;D;D;D;D

M_CAP

Pathogenic

0.72

MetaRNN

Pathogenic

0.99

D;D;D;D;D

MetaSVM

Pathogenic

1.1

MutationAssessor

Pathogenic

3.7

H;.;.;.;H

MutationTaster

Benign

1.0

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

PrimateAI

Uncertain

0.50

PROVEAN

Pathogenic

-9.4

D;D;D;D;D

REVEL

Pathogenic

0.92

Sift

Uncertain

0.0010

D;D;D;D;D

Sift4G

Pathogenic

0.0010

D;D;D;D;D

Polyphen

1.0

D;.;.;.;.

Vest4

0.91

MVP

1.0

MPC

0.82

ClinPred

1.0

GERP RS

5.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

Varity_R

0.96

gMVP

0.97

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

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