rs28942083

chr19-11120382-G-Achr19-11120382-G-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000527.5(LDLR):c.2000G>A(p.Cys667Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,850 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 Likely pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C667R) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000048 (0 hom.)
• Consequence: LDLR NM_000527.5 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:18
• Conservation: PhyloP100: 9.18

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 18 ACMG points.

• PM1: In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 10 uncertain in NM_000527.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr19-11120381-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 252163.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.995
• PP5: Variant 19-11120382-G-A is Pathogenic according to our data. Variant chr19-11120382-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 3689.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr19-11120382-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5	c.2000G>A	p.Cys667Tyr	missense_variant	14/18	ENST00000558518.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6	c.2000G>A	p.Cys667Tyr	missense_variant	14/18	1	NM_000527.5	P3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251394 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135888

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: 0.00000879

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000479 AC: 7 AN: 1461850 Hom.: 0 Cov.: 35 AF XY: 0.00000688 AC XY: 5 AN XY: 727220

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: 0.00000629

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000468 Hom.: 0

ExAC AF: 0.00000824 AC: 1

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:18

Revision: reviewed by expert panel

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:12

Likely pathogenic, criteria provided, single submitter	clinical testing	Robarts Research Institute, Western University	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	Mar 30, 2017	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 01, 1990	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Sep 04, 2020	The p.Cys667Tyr variant in LDLR has been reported in 15 heterozygotes with familial hypercholesterolemia (FH), one compound heterozygote with homozygous FH (HoFH), and three homozygous individuals with HoFH and segregated with disease in one affected individual (Leitersdorf 1990 PMID: 2318961, Cenarro 1998 PMID: 10206683, Gaudet 1999 PMID: 10208490, Fouchier 2001 PMID: 11810272, Mozas 2004 PMID: 15241806, Kubalska 2008 PMID: 18263977, Guardamagna 2009 PMID: 19446849, Chmara 2010 PMID: 20145306, Bertolini 2013 PMID: 23375686). The p.Cys667Tyr variant has also been identified in only 1/113720 European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant, which has been referred to as Cys646Tyr or FH French Canadian-2 (Leitersdorf 1990 PMID: 2318961, Bodamer 2002 PMID: 12406975) and reported in ClinVar (Variation ID 3689). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. Another variant involving this codon (p.Cys667Arg) has been identified in individuals with disease and is classified as likely pathogenic by this laboratory. Other variants involving this codon have also been noted in ClinVar but are less well-characterized (p.Cys667Trp, p.Cys667Phe, p.Cys667Ser). In vitro functional studies, including fibroblasts from a homozygous patient, demonstrate abnormal LDL receptor protein folding, trafficking, and conversion from the precursor to the mature protein (Leitersdorf 1990 PMID: 2318961). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant familial hypercholesterolemia. ACMG/AMP criteria applied: PS3, PS4_Moderate, PM2, PM3, PP3. -
Pathogenic, criteria provided, single submitter	clinical testing	Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute	-	- -
Likely pathogenic, criteria provided, single submitter	research	Fundacion Hipercolesterolemia Familiar	Mar 01, 2016	- -
Pathogenic, criteria provided, single submitter	research	Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	Mar 03, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 17, 2021	- -
Likely pathogenic, reviewed by expert panel	curation	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	Jun 18, 2021	NM_000527.5(LDLR):c.2000G>A (p.Cys667Tyr) variant is classified as Likely pathogenic for Familial Hypercholesterolemia by applying evidence codes (PM1, PM2, PS3_Moderate, PP3, PP4 and PS4_Supporting) 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: PM1 - Variant meets PM2 and is one of listed Cysteine. PM2 - PopMax MAF = 0.000008794 (0.0009%) in European non-Finnish exomes (gnomAD v2.1.1). PS3_moderate - PMID:2318961 - Level 2 assay - study on hmz patient's fibroblasts, after 2 hours pulse-chase, only 20% of receptors were processed to the mature form. Also here PMID: 14993243 and here PMID: 10906332 is shown that this mutant is retained on ER. In last two papers not whole LDLR cycle was studied. PP3 - REVEL: 0,986. PP4 - Variant meets PM2. Variant found in 5 unrelated index cases fulfilling validated clinical criteria for FH. PS4_supporting - Variant meets PM2. Variant identified in 5 unrelated index cases (1 case from Color laboratory with Simon-Broome criteria; 1 case from Ambry Genetics with Simon-Broome criteria; 1 case from GeneDx Inc. with Simon-Broome criteria; 2 cases from University of British Columbia with DLCN score 16 and 10, respectively). -
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 = 2 , family member = 1 with co-segregation / previously described in association with FH, < 2% LDLR Activity/software prediction damaging -
Likely pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -

Familial hypercholesterolemia Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 23, 2023	This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 667 of the LDLR protein (p.Cys667Tyr). This variant is present in population databases (rs28942083, gnomAD 0.0009%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 2318961, 10206683, 11810272, 15241806, 18263977, 23375686, 27765764). This variant is also known as p.Cys646Tyr. ClinVar contains an entry for this variant (Variation ID: 3689). 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: 2318961). This variant affects a cysteine residue located within an LDLRA or epidermal-growth-factor (EGF)-like domains of the LDLR protein. Cysteine residues in these domains have been shown to be involved in the formation of disulfide bridges, which are critical for protein structure and stability (PMID: 7548065, 7603991, 7979249). In addition, missense substitutions within the LDLRA and EGF-like domains affecting cysteine residues are overrepresented among patients with hypercholesterolemia (PMID: 18325082). This variant disrupts the p.Cys667 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been observed in individuals with LDLR-related conditions (PMID: 9412789, 11313767, 15701167, 24507775), which suggests that this may be a clinically significant amino acid residue. 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	Sep 14, 2023	Variant summary: LDLR c.2000G>A (p.Cys667Tyr) 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 4e-06 in 251394 control chromosomes. c.2000G>A has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia (e.g. Bertolini_2013, Bodamer_2002, Cenarro_1998, Leitersdorf_1990, Madar_2022, Kublaska_2008). Additionally, other missense variants in the same residue (p.C667F, p.C667R, p.C667S and p.C667W) have all been classified pathogenic/likely pathogenic in ClinVar, supporting the functional importance of this residue of the protein. 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 demonstrating effect on protein processing (Leitersdorf_1990). The following publications have been ascertained in the context of this evaluation (PMID: 23375686, 12406975, 10206683, 18263977, 35052492, 2318961). Twelve submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified 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	Color Diagnostics, LLC DBA Color Health	Aug 12, 2018	Pathogenic variant based on current evidence: This missense variant (also known as p.Cys646Tyr in the mature protein and as FH French Canadian-2) is located in the EGF-like repeat C of the EGF precursor homology 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 the RNA splicing. Experimental functional studies have shown that this variant abolishes maturation and transport of the LDLR protein to the cell surface (PMID: 2318961). While this variant is rare in the general population (1/246206 chromosomes in the Genome Aggregation Database (gnomAD)), this variant has been reported in over 30 individuals diagnosed with familial hypercholesterolemia (PMID: 2318961, 10206683, 11810272, 18263977, 25278291) and particularly common in the French Canadian population (PMID: 2318961). Based on available evidence this variant is classified as Pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 21, 2020	Reported multiple times in the heterozygous, compound heterozygous, and homozygous state in individuals with clinically diagnosed FH from various ethnic backgrounds; has also been reported as C646Y due to alternate nomenclature, and historically reported as FH French Canadian-2 (see examples: Leitersdorf et al., 1990; Cenarro et al., 1998; Foucheir et al., 2001; Mozas et al., 2004; Kublaska et al., 2008; Guardamagna et al., 2009; Chmara et al., 2010); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Located within the LDL-receptor EGF precursor domain and participates in disulfide bonding with another cysteine residue which is critical for correct protein structure (Sudhof et al., 1985; Rudenko et al., 2002); Published functional studies show that the C667Y variant results in abnormal LDL receptor protein folding and trafficking (Leitersdorf et al., 1990; Li et al., 2004; Srensen et al., 2006; Oka et al., 2013); This variant is associated with the following publications: (PMID: 12406975, 16257961, 17353666, 11213091, 31345425, 29407885, 32143996, 32807694, 14993243, 23375686, 11810272, 10906332, 2318961, 10206683, 1301956, 15241806, 10208489, 18263977, 19446849, 20145306, 23769672, 15556092, 28619117, 31447099, 32041611) -
Pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	May 26, 2021	- -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 13, 2018

The p.C667Y pathogenic mutation (also known as c.2000G>A), located in coding exon 14 of the LDLR gene, results from a G to A substitution at nucleotide position 2000. The cysteine at codon 667 is replaced by tyrosine, an amino acid with highly dissimilar properties. This mutation is found in the EGF precursor-like C domain of the LDLR gene. In the original report, this mutation, also known as p.C646Y, was identified as a Class 2 mutation, and in vitro functional analyses indicated this mutation caused significantly decreased LDL receptor activity suggesting abnormal LDL protein folding and transport (Leitersdorf E et al. J Clin Invest. 1990;85(4):1014-23). This mutation has been reported in several patients with familial hypercholesterolemia (FH) (Leitersdorf E et al. J Clin Invest. 1990;85(4):1014-23; Chmara M et al. J Appl Genet. 2010;51(1):95-106; Bertolini S et al. Atherosclerosis. 2013; 227(2):342-8). In one study, this mutation was described in conjunction with another mutation (p.G592E) in LDLR in a compound heterozygous patient with FH who initially presented with planar xanthomas at 6-12 months of age (Kubalska J et al. J Appl Genet. 2008;49(1):109-13). Furthermore, other alterations affecting the same codon (p.C667F c.2000G>T; p.C667R c.1999T>C; p.C667S c.1999T>A; p.C667W c.2001T>G; p.C667* c.2001T>A) have been described in patients with FH (Heath KE et al. Eu J Hum Genet. 2001;9(4):244-52; Vergopoulos A et al. Eur J Hum Genet. 1997;5(5):315-23; Zakharova FM et al. BMC Med Genet. 2005;6:6; Nissen H et al. Clin Genet. 1998;54(1):79-82; Ekstrom U et al. Hum Genet. 1995;96(2):147-50). Based on the supporting evidence, p.C667Y is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.59	D
BayesDel_noAF	Pathogenic	0.61
Cadd	Pathogenic	31
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.95	D;.;.;.;.
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.93
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.87	D;D;D;D;D
M_CAP	Pathogenic	0.97	D
MetaRNN	Pathogenic	1.0	D;D;D;D;D
MetaSVM	Pathogenic	0.98	D
MutationAssessor	Pathogenic	4.5	H;.;.;.;H
MutationTaster	Benign	1.0	D;D;D;D;D;D;D
PrimateAI	Uncertain	0.63	T
PROVEAN	Pathogenic	-10	D;D;D;D;D
Sift	Pathogenic	0.0	D;D;D;D;D
Sift4G	Uncertain	0.0020	D;D;D;D;D
Polyphen		1.0	D;.;.;.;.
Vest4		0.95
MutPred		0.97		Loss of catalytic residue at C667 (P = 0.1768);Loss of catalytic residue at C667 (P = 0.1768);.;.;Loss of catalytic residue at C667 (P = 0.1768);
MVP		1.0
MPC		1.1
ClinPred		1.0	D
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		1.0
gMVP		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs28942083; hg19: chr19-11231058;