Total submissions: 44
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Clin |
RCV000172964 | SCV001960930 | pathogenic | Hypercholesterolemia, familial, 1 | 2021-06-09 | reviewed by expert panel | curation | NM_000527.5(LDLR):c.1775G>A (p.Gly592Glu) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PS4, PP1_Strong, PM2, PS3_Moderate, 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: PS4 - Variant meets PM2. Variant identified in 239 index cases. PP1_strong - 130 informative meioses (1 from Robarts Research Institute; 83 from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); 19 from Laboratory of Genetics and Molecular Cardiology; 2 from University of British Columbia; 25 from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge). PM2 - PopMax MAF = 0.0001161 (0.012%) in European non-Finnish exomes (gnomAD v2.1.1). PS3_moderate - Level 2 assay - PMID:21865347 - study on hmz patient's lymphocytes, FACS, LDLR activity value range: 39-53%. PP3 - REVEL: 0,938. PP4 - Variant meets PM2. Variant identified in 239 index cases fulfill specific clinical criteria for FH (3 cases with Simon-Broome from Color laboratory; 189 cases with MedPed criteria from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); 5 cases with Simon-Broome criteria from GeneDx; 15 cases with Siom-Broome criteria from Laboratory of Genetics and Molecular Cardiology; 2 cases with DLCN criteria from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA); 6 cases with DLCN criteria from University of British Columbia; 19 cases with Simon-Broome criteria from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge). |
Institute for Integrative and Experimental Genomics, |
RCV000172964 | SCV000212140 | likely pathogenic | Hypercholesterolemia, familial, 1 | criteria provided, single submitter | research | ||
Laboratory for Molecular Medicine, |
RCV000844730 | SCV000271385 | pathogenic | Homozygous familial hypercholesterolemia | 2020-09-04 | criteria provided, single submitter | clinical testing | The p.Gly592Glu variant in LDLR has been reported in >200 Caucasian individuals with familial hypercholesterolemia (FH) and segregated with disease in >30 affected relatives from >3 families (Gorski 1998 PMID: 9654205, Miltiadous 2001 PMID: 11317361, Kuhrova 2002 PMID: 11754108, Kublaska 2008 PMID: 18263977, Bourbon 2008 PMID: 17765246, Chmara 2010 PMID: 20145306, Diakou 2011 PMID: 21925044, Tichy 2012 PMID: 22698793, Bertolini 2013 PMID: 23375686, Do 2015 PMID: 25487149, Medeiros 2015 PMID: 26020417, Jannes 2015 PMID: 25461735, Braenne 2015 PMID: 26036859). This variant has also been identified in 0.01% (15/129176) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org); however, this frequency is low enough to be consistent with the frequency of FH in the general population. Furthermore, in vitro functional studies support that the p.Gly592Glu variant may impact protein function (Romano 2011 PMID: 21865347). In summary, this variant meets criteria to be classified as pathogenic for familial hypercholesterolemia in an autosomal dominant manner based upon presence in multiple affected individuals and segregation studies. ACMG/AMP Criteria applied: PS4, PP1_Strong, PS3_Supporting. |
LDLR- |
RCV000172964 | SCV000295649 | likely pathogenic | Hypercholesterolemia, familial, 1 | 2016-03-25 | criteria provided, single submitter | literature only | |
Cardiovascular Research Group, |
RCV000172964 | SCV000322975 | likely pathogenic | Hypercholesterolemia, familial, 1 | 2016-03-01 | criteria provided, single submitter | research | 0/220 non-FH alleles; 0/77 healthy control individuals |
Robarts Research Institute, |
RCV000172964 | SCV000484718 | likely pathogenic | Hypercholesterolemia, familial, 1 | criteria provided, single submitter | clinical testing | ||
Centre de Génétique Moléculaire et Chromosomique, |
RCV000172964 | SCV000503412 | likely pathogenic | Hypercholesterolemia, familial, 1 | 2016-12-16 | criteria provided, single submitter | clinical testing | subjects mutated among 2600 FH index cases screened = 11 , family members = 3 with co-segregation / previously described in association with FH, 5 to 15% LDLR Activity/software prediction damaging |
Molecular Genetics Laboratory, |
RCV000172964 | SCV000540837 | likely pathogenic | Hypercholesterolemia, familial, 1 | 2016-11-05 | criteria provided, single submitter | clinical testing | |
Invitae | RCV000587007 | SCV000544669 | pathogenic | Familial hypercholesterolemia | 2024-01-28 | criteria provided, single submitter | clinical testing | This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 592 of the LDLR protein (p.Gly592Glu). This variant is present in population databases (rs137929307, gnomAD 0.01%). This missense change has been observed in individual(s) with familial hypercholesterolemia (PMID: 15864114, 20663204, 21310417). 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: 21925044, 23375686, 26238499). This variant is also known as p.Gly571Glu. ClinVar contains an entry for this variant (Variation ID: 161271). 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. |
Gene |
RCV000162001 | SCV000582282 | pathogenic | not provided | 2023-03-19 | criteria provided, single submitter | clinical testing | Published functional studies demonstrate that G592E results in reduced LDL receptor activity (Hobbs et al., 1992); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); Also known as p.G571E, FH Sicily, FH Foggi, FH Naples-4; This variant is associated with the following publications: (PMID: 27998977, 11524740, 24627126, 25282520, 34167030, 32423031, 35339733, 34697415, 21310417, 15864114, 26238499, 11641914, 22390909, 25637381, 21865347, 20145306, 26036859, 20663204, 15523646, 11848618, 26666465, 27824480, 21382890, 27050191, 19062533, 27578104, 25463123, 27784735, 22294733, 22698793, 26020417, 26892515, 15890894, 23833242, 18263977, 25487149, 16627557, 25936317, 23375686, 24507775, 26723464, 28965616, 15241806, 19026292, 17539906, 9654205, 17196209, 11139254, 20506408, 11754108, 11317361, 31617323, 31447099, 21925044, 33975813, 33303402, 32719484, 32660911, 33269076, 32770674, 32977124, 31589614, 32041611, 33740630, 33418990, 34037665, 34456049, 32009526, 35741760, 35913489, 33955087, 30710474, 1301956) |
U4M - |
RCV000172964 | SCV000583883 | pathogenic | Hypercholesterolemia, familial, 1 | 2017-03-30 | criteria provided, single submitter | clinical testing | |
Laboratory of Genetics and Molecular Cardiology, |
RCV000172964 | SCV000588605 | likely pathogenic | Hypercholesterolemia, familial, 1 | 2016-03-01 | criteria provided, single submitter | research | |
Fundacion Hipercolesterolemia Familiar | RCV000172964 | SCV000607638 | likely pathogenic | Hypercholesterolemia, familial, 1 | 2016-03-01 | criteria provided, single submitter | research | |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000587007 | SCV000697209 | pathogenic | Familial hypercholesterolemia | 2016-09-13 | criteria provided, single submitter | clinical testing | Variant summary: The LDLR c.1775G>A (p.Gly592Glu) variant involves the alteration of a conserved nucleotide. Gly592 is highly conserved across species, and 5/5 in silico tools predict a damaging outcome for this variant. This variant was found in 6/121608 control chromosomes at a frequency of 0.0000493, which does not exceed the estimated maximal expected allele frequency of a pathogenic LDLR variant (0.0025031). This variant has been reported in many FH patients in both heterozygous, compound heterozygous, and homozygous states with evidence of co-segregation in some of the families. Functional studies indicate that the variant of interest has defective LDL receptor activity. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic/likely pathogenic. Taken together, this variant is classified as pathogenic. |
Iberoamerican FH Network | RCV000172964 | SCV000748115 | likely pathogenic | Hypercholesterolemia, familial, 1 | 2016-03-01 | criteria provided, single submitter | research | |
Hudson |
RCV000172964 | SCV000778604 | pathogenic | Hypercholesterolemia, familial, 1 | 2018-02-27 | criteria provided, single submitter | research | |
Quest Diagnostics Nichols Institute San Juan Capistrano | RCV000162001 | SCV000888163 | pathogenic | not provided | 2022-04-08 | criteria provided, single submitter | clinical testing | Internal analysis revealed that the variant was statistically enriched in familial hypercholesterolemia cases over matched controls in the published literature (PMID: 17765246 (2008), 20145306 (2010), 21925044 (2011), 22698793 (2012), and 23375686 (2013)). Additionally, reduced LDL receptor activity was observed from fibroblasts and peripheral blood T-lymphocytes extracted from patients with this variant ((PMID: 1301956 (1992) and 21865347 (2011)). |
Fulgent Genetics, |
RCV000172964 | SCV000894177 | pathogenic | Hypercholesterolemia, familial, 1 | 2018-10-31 | criteria provided, single submitter | clinical testing | |
Color Diagnostics, |
RCV000587007 | SCV000903573 | pathogenic | Familial hypercholesterolemia | 2024-01-02 | criteria provided, single submitter | clinical testing | This missense variant replaces glycine with glutamic acid at codon 592 in the fifth LDLR type B repeat of the LDLR protein. This variant is also known as p.Gly571Glu in the mature protein and as FH-Sicily, FH Foggia-1, FH Naples. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). A functional study has shown that this variant results in a partial loss of LDLR activity (PMID: 21865347). The variant has been identified in over 200 heterozygous and homozygous familial hypercholesterolemia patients from multiple European ethnicities (PMID: 1301956, 9654205, 11139254, 11139254, 11317361, 11641914, 11754108, 15199436, 15241806, 17765246, 18263977, 20145306, 20663204, 21310417, 21925044, 22698793, 23375686, 25461735, 25463123, 25487149, 26020417, 31947532, 35741760). This variant is highly recurrent in Slovakia, Czech Republic, and Poland (PMID: 26238499). A different variant occurring at the same codon, p.Gly592Arg, is a likely pathogenic mutation (Clinvar variation ID: 373769), indicating that glycine at this position is important for LDLR protein function. This variant has been identified in 16/282866 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. |
Department of Human Genetics, |
RCV000172964 | SCV000987017 | pathogenic | Hypercholesterolemia, familial, 1 | 2018-10-29 | criteria provided, single submitter | clinical testing | This nucleotide substitution causes an exchange of the amino acid of glycine (Gly) to glutamic acid (Glu) p.Gly592Glu (legacy name: p.Gly571Glu). This change has already been described in the literature as FH Sicily, FH Foggia 1 and FH Naples 4 and has been found in patients with familial hypercholesterolemia and is associated with elevated cholesterol and LDL-C levels. It results in a reduced amount of biologically active LDL receptors on the cell surface. We observed this variant in a patient with TC up to 350 mg/dl and LDL-C approx 290 mg/dl at the age of 48 and in a patient with TC up to 300 mg/dl and LDL-C approx 250 mg/dl at the age of 5. PMID: 1301956, 27998977, 22390909, 26036859. |
UCSF Pediatric Lipid Clinic, |
RCV000172964 | SCV000998546 | pathogenic | Hypercholesterolemia, familial, 1 | criteria provided, single submitter | clinical testing | The p.G592E variant in LDLR segregates with elevated level of LDL-C in a family of over ten individuals. The allele frequency of this variant in the population is 0.00004 based on the GnomAD database. | |
Institute of Human Genetics, |
RCV000172964 | SCV001429254 | pathogenic | Hypercholesterolemia, familial, 1 | 2023-08-15 | criteria provided, single submitter | clinical testing | Criteria applied: PS4,PP1_STR,PS3_MOD,PM5,PM2_SUP,PP3 |
Brunham Lab, |
RCV000172964 | SCV001432593 | pathogenic | Hypercholesterolemia, familial, 1 | 2019-03-03 | criteria provided, single submitter | research | |
Laboratory of Molecular Genetics, |
RCV000587007 | SCV001482461 | likely pathogenic | Familial hypercholesterolemia | criteria provided, single submitter | research | ||
Laboratory of molecular diagnosis of dyslipidemias, |
RCV000172964 | SCV001653652 | likely pathogenic | Hypercholesterolemia, familial, 1 | 2021-05-24 | criteria provided, single submitter | clinical testing | Reduced activity, in stimulated T-lymphocytes and EBV-transformed B-lymphocytes. |
Ai |
RCV000162001 | SCV002503265 | pathogenic | not provided | 2022-02-23 | criteria provided, single submitter | clinical testing | |
Institute of Human Genetics, |
RCV002051664 | SCV002506438 | pathogenic | Hypercholesterolemia | 2021-12-15 | criteria provided, single submitter | clinical testing | ACMG categories: PS3,PM1,PP1,PP3,PP4,PP5 |
Laan Lab, |
RCV000172964 | SCV002538607 | pathogenic | Hypercholesterolemia, familial, 1 | 2021-05-01 | criteria provided, single submitter | research | |
MGZ Medical Genetics Center | RCV000172964 | SCV002580733 | pathogenic | Hypercholesterolemia, familial, 1 | 2022-08-26 | criteria provided, single submitter | clinical testing | |
Ambry Genetics | RCV002399517 | SCV002714823 | pathogenic | Cardiovascular phenotype | 2021-09-21 | criteria provided, single submitter | clinical testing | The p.G592E pathogenic mutation (also known as c.1775G>A), located in coding exon 12 of the LDLR gene, results from a G to A substitution at nucleotide position 1775. The glycine at codon 592 is replaced by glutamic acid, an amino acid with some similar properties, and is located in the EGF precursor-like domain. This mutation, also known as FH-Sicily and G571E, has been detected in many unrelated individuals with familial hypercholesterolemia (FH), and has also been reported to impact protein function (Hobbs et al. Hum Mutat. 1992;1(6):445-66; Miltiadous G et al. Hum Mutat. 2001;17(5):432-3; Romano M et al. J Lipid Res. 2011;52(11):2095-100; Susan-Resiga D et al. J Biol Chem. 2017;292(5):1573-1590). In addition, this mutation has been reported as one of the most common amongst Czech, Polish, German, Austrian, and Slovak FH cohorts (Chmara M et al. J Appl Genet. 2010;51(1):95-106; Tichy et al. Atherosclerosis. 2012;223(2):401-8; Gabová D et al. Physiol Res. 2017;66(1):75-84). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. |
Revvity Omics, |
RCV000172964 | SCV003827125 | pathogenic | Hypercholesterolemia, familial, 1 | 2022-11-18 | criteria provided, single submitter | clinical testing | |
Baylor Genetics | RCV000172964 | SCV003836115 | pathogenic | Hypercholesterolemia, familial, 1 | 2021-12-29 | criteria provided, single submitter | clinical testing | |
Ce |
RCV000162001 | SCV003918065 | pathogenic | not provided | 2024-03-01 | criteria provided, single submitter | clinical testing | LDLR: PP1:Strong, PM2, PM5, PS4:Moderate, PP4, PS3:Supporting |
Institute for Medical Genetics and Human Genetics, |
RCV003330084 | SCV004037152 | likely pathogenic | Syndromic X-linked intellectual disability Najm type | criteria provided, single submitter | not provided | ||
Mayo Clinic Laboratories, |
RCV000162001 | SCV004227680 | pathogenic | not provided | 2022-06-02 | criteria provided, single submitter | clinical testing | PP1_strong, PP3, PP4, PM2, PS3, PS4 |
All of Us Research Program, |
RCV000172964 | SCV004822500 | pathogenic | Hypercholesterolemia, familial, 1 | 2024-01-04 | criteria provided, single submitter | clinical testing | This missense variant (also known as p.Gly571Glu in the mature protein and as FH-Sicily, FH Foggia-1, FH Naples) is located in the fifth LDLR type B repeat of the LDLR protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). A functional study has shown that this variant results in a partial loss of LDLR activity (PMID: 21865347). The variant has been identified in over 200 heterozygous and homozygous familial hypercholesterolemia patients from multiple European ethnicities (PMID: 1301956, 9654205, 11139254, 11139254, 11317361, 11641914, 11754108, 15199436, 15241806, 17765246, 18263977, 20145306, 20663204, 21310417, 21925044, 22698793, 23375686, 25461735, 25463123, 25487149, 26020417, 31947532, 35741760). This variant is highly recurrent in Slovakia, Czech Republic, and Poland (PMID: 26238499). A different variant occurring at the same codon, p.Gly592Arg, is a likely pathogenic mutation (Clinvar variation ID: 373769), indicating that glycine at this position is important for LDLR protein function. This variant has been identified in 16/282866 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. |
Dept. |
RCV000162001 | SCV000189576 | not provided | not provided | no assertion provided | in vitro | ||
CSER _CC_NCGL, |
RCV002051664 | SCV000190290 | pathogenic | Hypercholesterolemia | 2014-06-01 | no assertion criteria provided | research | |
Cardiovascular Genetics Laboratory, |
RCV000172964 | SCV000268637 | pathogenic | Hypercholesterolemia, familial, 1 | 2010-09-07 | no assertion criteria provided | clinical testing | |
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, |
RCV000172964 | SCV000606511 | pathogenic | Hypercholesterolemia, familial, 1 | no assertion criteria provided | research | ||
Diagnostic Laboratory, |
RCV000162001 | SCV000733827 | pathogenic | not provided | no assertion criteria provided | clinical testing | ||
Natera, |
RCV000587007 | SCV001461319 | pathogenic | Familial hypercholesterolemia | 2020-09-16 | no assertion criteria provided | clinical testing | |
Clinical Genetics, |
RCV000162001 | SCV001918371 | pathogenic | not provided | no assertion criteria provided | clinical testing | ||
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, |
RCV000162001 | SCV001951679 | pathogenic | not provided | no assertion criteria provided | clinical testing |