19-11102732-T-G

Position:

• chr19-11102732-T-G

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PP1_Moderate PM2 PP3 PP4 PS4 PS3

This summary comes from the ClinGen Evidence Repository: The NM_000527.5(LDLR):c.259T>G (p.Trp87Gly) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PS3, PS4, PP1_Moderate, PM2, PP3 and PP4) 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: PS3 - Level 1/2 assays: PMID 31578082: Hmz patients' lymphocytes, FACS assays and Heterologous cells (CHO), WB, FACS and CLSM assays - results - lymphocytes: normal cell surface LDLR, 40% LDL-LDLR binding, 35% uptake; CHO: normal (100%) LDLR expression, 20% LDL-LDLR binding, 35% uptake ---- binding and uptake are below 70% of wild-type, so PS3 is Met.PS4 - Variant meets PM2. Variant identified in at least 13 unrelated index cases with Dutch Lipid Clinic score equal or above 6 from different labs.PP1_moderate - variant segregates with FH phenotype in 5 informative meiosis in 2 families from different labs.PM2 - PopMax MAF = 0.00005418 (0.0054%) in european non-finnish exomes (gnomAD v2.1.1).PP3 - REVEL = 0.892. PP4 - Variant meets PM2. Identified in 13 unrelated index cases with Dutch Lipid Clinic score equal or above 6 from different labs. LINK:https://erepo.genome.network/evrepo/ui/classification/CA023683/MONDO:0007750/013

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000016 (0 hom.)
• Consequence: LDLR NM_000527.5 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:27
• Conservation: PhyloP100: 6.03

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 Pathogenic. Variant got 14 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LDLR	NM_000527.5	c.259T>G	p.Trp87Gly	missense_variant	3/18	ENST00000558518.6	NP_000518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LDLR	ENST00000558518.6	c.259T>G	p.Trp87Gly	missense_variant	3/18	1	NM_000527.5	ENSP00000454071	P3

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152172 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000656

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: 0.0000278 AC: 7 AN: 251490 Hom.: 0 AF XY: 0.0000221 AC XY: 3 AN XY: 135922

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000615

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000157 AC: 23 AN: 1461740 Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7 AN XY: 727170

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000207

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152172 Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1 AN XY: 74336

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000656

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: 0.0000332 Hom.: 0

Bravo AF: 0.00000378

ExAC AF: 0.0000412 AC: 5

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:27

Revision: reviewed by expert panel

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:16

Pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Feb 04, 2020	The c.259T>G (p.Trp87Gly) variant in the LDLR gene has been reported in multiple individuals with familial hypercholesterolemia (PMID: 2318961, 8054972, 8645371, 9259195, 9104431). It is located in the functionally important second LDLR type A repeat. Functional studies have demonstrated a deleterious effect of the p.Trp87Gly variant on LDL binding (PMID: 2318961, 8645371, 10735631). The variant is observed in gnomAD at a low minor allele frequency (8/282882). Multiple algorithms predicted this change to be deleterious. Therefore, the c.259T>G (p.Trp87Gly) variant in the LDLR gene is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	Mar 30, 2017	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	Jun 07, 2021	The NM_000527.5(LDLR):c.259T>G (p.Trp87Gly) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PS3, PS4, PP1_Moderate, PM2, PP3 and PP4) 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: PS3 - Level 1/2 assays: PMID 31578082: Hmz patients' lymphocytes, FACS assays and Heterologous cells (CHO), WB, FACS and CLSM assays - results - lymphocytes: normal cell surface LDLR, 40% LDL-LDLR binding, 35% uptake; CHO: normal (100%) LDLR expression, 20% LDL-LDLR binding, 35% uptake ---- binding and uptake are below 70% of wild-type, so PS3 is Met. PS4 - Variant meets PM2. Variant identified in at least 13 unrelated index cases with Dutch Lipid Clinic score equal or above 6 from different labs. PP1_moderate - variant segregates with FH phenotype in 5 informative meiosis in 2 families from different labs. PM2 - PopMax MAF = 0.00005418 (0.0054%) in european non-finnish exomes (gnomAD v2.1.1). PP3 - REVEL = 0.892. PP4 - Variant meets PM2. Identified in 13 unrelated index cases with Dutch Lipid Clinic score equal or above 6 from different labs. -
Likely pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	May 20, 2021	PS4, PM2_Supporting, PP3, PM1, PS3_Moderate -
Pathogenic, criteria provided, single submitter	clinical testing	Johns Hopkins Genomics, Johns Hopkins University	May 28, 2021	This variant (rs121908025) is rare (<0.1%) in a large population database (gnomAD: 8/282882 total alleles, 0.003%, no homozygotes) and has an entry in ClinVar. It has been reported in multiple individuals with familial hypercholesterolemia-1, and is considered a founder mutation in the French-Canadian population. This variant is located in the second type A repeat of the ligand binding domain of the LDLR protein. Functional studies have demonstrated a deleterious effect of p.Trp87Gly on LDL binding and uptake. This variant was also identified in the patient's father, who has a personal history of elevated cholesterol. We consider c.259T>G to be pathogenic. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 01, 1994	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 14, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Dec 18, 2023	This missense variant (also known as p.Trp66Gly in the mature protein) is located in the second LDLR type A repeat of the ligand binding domain of the LDLR protein. Computational prediction tools and conservation analyses suggest that this variant may have deleterious impact on the protein function. Computational splicing tools suggest that this variant may not impact RNA splicing. Experimental studies have demonstrated that the variant protein showed reduced LDL binding (PMID: 8645371, 10735631, 31578082). This variant has been identified in over 500 individuals affected with familial hypercholesterolemia (PMID: 2318961, 8098448, 9104431, 9259195, 9272705, 9676383, 12553167, 15528480, 16542394, 23669246, 30512145, 31345425, 31578082, 33955087). This variant is common in individuals of European descent and is considered a founder mutation in the French-Canadian population (PMID: 9272705) and Swedish population (PMID: 33955087). Homozygous individuals have shown much higher LDL-C levels than heterozygous individuals (PMID: 8098448). This variant has been identified in 8/282882 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on available evidence, this variant is classified as Pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital	Dec 18, 2008	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Dec 06, 2023	Criteria applied: PS3,PS4,PP1_MOD,PM2_SUP,PP3,PP4 -
Likely pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation	Nov 05, 2016	- -
Pathogenic, criteria provided, single submitter	research	Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	Mar 13, 2019	- -
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	-	- -
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	subjects mutated among 2600 FH index cases screened = 9 , family members = 7 with co-segregation / frequently associated with c.1975A>C, p.Thr659Pro (2 index cases), Subnormal LDLR activity / Software predictions: Damaging -

not provided Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 19, 2022	LDL receptor activity was significantly reduced in the fibroblasts from two of three unrelated individuals who were homozygous for the FH French Canadian-4 allele (Hobbs et al., 1992) and this variant affects either LDLR turnover or the binding of the LDLR protein to LDL (Leitersdorf et al., 1990); 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: 28008010, 9104431, 2318961, 9259195, 8645371, 15528480, 23669246, 24281370, 9767373, 12381843, 30586733, 30512145, 29874871, 29261184, 31401775, 29407885, 31727422, 34040191, 32041611, 33303402, 32719484, 32770674, 33740630, 34037665, 33087929, 9272705, 1301956, 16542394) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Mar 07, 2023	PP3, PP4, PM2_supporting, PM3, PS3_supporting, PS4 -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2024	LDLR: PM1, PM2, PP1:Moderate, PS4:Moderate, PP4, PS3:Supporting -
Likely pathogenic, criteria provided, single submitter	clinical testing	Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute	Jul 11, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	Jun 30, 2023	- -

Familial hypercholesterolemia Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 24, 2023	This missense variant (also known as p.Trp66Gly in the mature protein) is located in the second LDLR type A repeat of the ligand binding domain of the LDLR 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). Experimental functional studies have demonstrated that the variant protein showed reduced LDL binding (PMID: 8645371, 10735631, 31578082). This variant has been identified in over 500 individuals affected with familial hypercholesterolemia (PMID: 2318961, 8098448, 9104431, 9259195, 9272705, 9676383, 12553167, 15528480, 16542394, 23669246, 30512145, 31345425, 31578082, 33955087, 34037665). This variant is common in individuals of European descent and is considered a founder mutation in the French-Canadian population (PMID: 9272705) and Swedish population (PMID: 33955087). Homozygous individuals have shown much higher LDL-C levels than heterozygous individuals (PMID: 8098448, 36727130). This variant has been identified in 8/282882 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 02, 2024	This sequence change replaces tryptophan, which is neutral and slightly polar, with glycine, which is neutral and non-polar, at codon 87 of the LDLR protein (p.Trp87Gly). This variant is present in population databases (rs121908025, gnomAD 0.006%). This missense change has been observed in individual(s) with familial hypercholesterolemia (PMID: 2318961, 12553167, 16542394). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It is commonly reported in individuals of European ancestry (PMID: 2318961, 12553167, 16542394). This variant is also known as p.W66G. ClinVar contains an entry for this variant (Variation ID: 3685). 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: 8098448). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 14, 2020	Variant summary: LDLR c.259T>G (p.Trp87Gly) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.8e-05 in 251490 control chromosomes. c.259T>G has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia (e.g. Leitersdorf_1990, Moorjani_1993, Banerjee_2019). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, indicating the cells expressing the variant have reduced LDL-binding and uptake (e.g. Banerjee_2019). 11 clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories cited the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	Feb 04, 2020	The c.259T>G (p.Trp87Gly) variant in the LDLR gene has been reported in multiple individuals with familial hypercholesterolemia (PMID: 2318961, 8054972, 8645371, 9259195, 9104431). It is located in the functionally important second LDLR type A repeat. Functional studies have demonstrated a deleterious effect of the p.Trp87Gly variant on LDL binding (PMID: 2318961, 8645371, 10735631). The variant is observed in gnomAD at a low minor allele frequency (8/282882). Multiple algorithms predicted this change to be deleterious. Therefore, the c.259T>G (p.Trp87Gly) variant in the LDLR gene is classified as pathogenic. -

Homozygous familial hypercholesterolemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2019

The p.Trp87Gly variant in LDLR is a well-established pathogenic variant for familial hypercholesterolemia (Leitersdorf 1990, Jensen 1996, Vohl 1997, Tybjaerg-Hansen 2005, Futema 2013), and is a known founder mutation in the French Canadian population where it has been reported in >400 individuals with FH, including >15 homozygous individuals (Vohl 1997). It has also been identified in 5/66740 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs121908025); however, this frequency is low enough to be consistent with the frequency of FH in the general population. Additionally, in vitro functional studies provide some evidence that the p.Trp87Gly variant may impact protein function (Leitersdorf 1990). In summary, this variant meets our criteria to be classified as pathogenic for FH in an autosomal dominant manner based upon its identification in a large number of affected individuals and low frequency in controls. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 26, 2022

The p.W87G pathogenic mutation (also known as c.259T>G), located in coding exon 3 of the LDLR gene, results from a T to G substitution at nucleotide position 259. The tryptophan at codon 87 is replaced by glycine, an amino acid with highly dissimilar properties. This mutation, historically reported as W66G, has been identified in multiple individuals with familial hypercholesterolemia (FH) (Leitersdorf E et al. J. Clin. Invest., 1990 Apr;85:1014-23; Brusgaard K et al. Clin. Genet., 2006 Mar;69:277-83; Langsted A et al. Lancet Diabetes Endocrinol, 2016 Jul;4:577-87). This alteration has been reported in FH patients across ethnic groups and has been designated a founder mutation in the French Canadian and Danish populations (Vohl MC et al. Clin. Genet., 1997 Jul;52:1-6; Jensen HK et al. Atherosclerosis, 1999 Oct;146:337-44). In vitro functional studies have demonstrated that this mutation causes defects in cell surface binding of LDL (Leitersdorf E et al. J. Clin. Invest., 1990 Apr;85:1014-23; Raungaard B et al. Clin. Genet., 2000 Feb;57:110-5). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.90
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.54
CADD	Pathogenic	31
DANN	Uncertain	0.98
DEOGEN2	Pathogenic	0.95	D;.;.;.;.
Eigen	Uncertain	0.68
Eigen_PC	Uncertain	0.63
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.92	D;D;D;D;D
M_CAP	Pathogenic	0.93	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.2	M;.;M;M;M
MutationTaster	Benign	1.0	D;D;D;D;D;D;N
PrimateAI	Uncertain	0.57	T
PROVEAN	Pathogenic	-12	D;D;D;D;D
REVEL	Pathogenic	0.89
Sift	Pathogenic	0.0	D;D;T;D;D
Sift4G	Pathogenic	0.0	D;D;T;D;D
Polyphen		1.0	D;.;.;.;.
Vest4		0.81
MutPred		0.73		Loss of stability (P = 0.0576);Loss of stability (P = 0.0576);Loss of stability (P = 0.0576);Loss of stability (P = 0.0576);Loss of stability (P = 0.0576);
MVP		0.98
MPC		1.1
ClinPred		1.0	D
GERP RS		5.7
Varity_R		0.98
gMVP		0.98

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: rs121908025; hg19: chr19-11213408;