Submissions for variant NM_000527.5(LDLR):c.1783C>T (p.Arg595Trp)

Total submissions: 27

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	RCV000237585	SCV001960931	pathogenic	Hypercholesterolemia, familial, 1	2021-06-09	reviewed by expert panel	curation	NM_000527.5(LDLR):c.1783C>T (p.Arg595Trp) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PS4, PP1_Strong, 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: PS4 - Variant meets PM2. Variant identified in 12 index cases. PP1_strong - 10 informative meioses identified by Laboratory of Genetics and Molecular Cardiology. PM2 - PopMax MAF = 0.00001548 (0.0015%) in European non-Finnish (gnomAD v2.1.1). PP3 - REVEL: 0,89. PP4 - Variant meets PM2. Variant identified in 12 index cases fulfilling validated clinical criteria for FH (6 cases with Simon-Broome or DLCN criteria from Ambry Genetics; 2 cases with Simon-Broome from Color laboratory; 3 cases with Simon-Broome criteria from Laboratory of Genetics and Molecular Cardiology; 1 case with Simon-Broome criteria from GeneDx).
LDLR-LOVD, British Heart Foundation	RCV000237585	SCV000295653	likely pathogenic	Hypercholesterolemia, familial, 1	2016-03-25	criteria provided, single submitter	literature only
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	RCV000237585	SCV000494601	pathogenic	Hypercholesterolemia, familial, 1	2017-03-30	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	RCV000237585	SCV000503414	likely pathogenic	Hypercholesterolemia, familial, 1	2016-12-16	criteria provided, single submitter	clinical testing	subject mutated among 2600 FH index cases screened = 1 / previously described in association with FH/software prediction damaging
Laboratory of Genetics and Molecular Cardiology, University of São Paulo	RCV000237585	SCV000588606	uncertain significance	Hypercholesterolemia, familial, 1	2016-03-01	criteria provided, single submitter	research
Fundacion Hipercolesterolemia Familiar	RCV000237585	SCV000607640	uncertain significance	Hypercholesterolemia, familial, 1	2016-03-01	criteria provided, single submitter	research
Athena Diagnostics	RCV000518174	SCV000614004	likely pathogenic	not provided	2017-06-16	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000588105	SCV000697210	pathogenic	Familial hypercholesterolemia	2019-09-30	criteria provided, single submitter	clinical testing	Variant summary: LDLR c.1783C>T (p.Arg595Trp) results in a non-conservative amino acid change in 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 251488 control chromosomes. c.1783C>T has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia in the homozygous and compound heterozygous state (Mozas_2004, Junyent_2010, Damgaard_2005, Chiou_2012, Pek_2018, Pirillo_2017). 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. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments, three as VUS, six as likely pathogenic/pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Iberoamerican FH Network	RCV000237585	SCV000748099	uncertain significance	Hypercholesterolemia, familial, 1	2016-03-01	criteria provided, single submitter	research
Labcorp Genetics (formerly Invitae), Labcorp	RCV000588105	SCV000752411	pathogenic	Familial hypercholesterolemia	2023-12-01	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 595 of the LDLR protein (p.Arg595Trp). This variant is present in population databases (rs373371572, gnomAD 0.002%). This missense change has been observed in individuals with familial hypercholesterolaemia (PMID: 11737238, 16250003, 20538126, 25461735, 27784735). ClinVar contains an entry for this variant (Variation ID: 161290). 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%. This variant disrupts the p.Arg595 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15256764, 15359125, 16250003, 18718593, 25437892, 25487149, 27497240, 28502510). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Color Diagnostics, LLC DBA Color Health	RCV000588105	SCV000909180	pathogenic	Familial hypercholesterolemia	2023-04-20	criteria provided, single submitter	clinical testing	This missense variant (also known as p.Arg574Trp in the mature protein) replaces arginine with tryptophan at codon 595 in the fifth LDLR type B repeat of the EGF precursor homology 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). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in over 20 individuals affected with familial hypercholesterolemia (PMID: 11737238, 16250003, 20538126, 25461735, 28502510, 32044282, 32331935, 34037665, 34176852; Color internal data), including three homozygous individuals with severe phenotype (PMID: 27784735). This variant has been identified in 2/282862 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different missense variants occurring at the same codon (p.Arg595Leu and Arg595Gln) have been reported in individuals affected with familial hypercholesterolemia (ClinVar variation ID: 252029, 183126), suggesting that arginine at this position is a functionally and clinically important residue. Based on the available evidence, this variant is classified as Pathogenic.
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	RCV000237585	SCV001149823	likely pathogenic	Hypercholesterolemia, familial, 1	2018-12-27	criteria provided, single submitter	clinical testing
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute	RCV000518174	SCV001433287	likely pathogenic	not provided	2020-03-16	criteria provided, single submitter	clinical testing
Institute of Human Genetics, University of Leipzig Medical Center	RCV000237585	SCV001440210	uncertain significance	Hypercholesterolemia, familial, 1	2020-09-07	criteria provided, single submitter	clinical testing
DASA	RCV000588105	SCV002097311	pathogenic	Familial hypercholesterolemia	2022-02-14	criteria provided, single submitter	clinical testing	The c.1783C>T;p.(Arg595Trp) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar: 161290; PMID: 11737238; 25461735; 27784735; 16250003; 20538126) - PS4. The variant is located in a mutational hot spot and/or critical and well-established functional domain (Ldl_recept_b) - PM1. The variant is present at low allele frequencies population databases (rs373371572 - gnomAD 0.0002631%; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2_supporting. Pathogenic missense variant in this residue have been reported (ClinVar ID: 252029 - c.1784G>T;p.(Arg595Leu)) - PM5. The variant co-segregated with disease in multiple affected family members (PMID: 11737238; 16250003; 20538126) - PP1_strong. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is pathogenic.
GeneDx	RCV000518174	SCV002526489	pathogenic	not provided	2022-10-07	criteria provided, single submitter	clinical testing	Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Reported as a pathogenic variant by ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel (ClinVar Variant ID#171218; SCV001960931.1); Also known as p.(R574W); This variant is associated with the following publications: (PMID: 25637381, 28502510, 29172679, 28965616, 15823288, 16250003, 28502495, 30586733, 31491741, 31447099, 33740630, 34037665, 29353225, 32331935, 11737238, 15241806, 27578128, 30583242, 34906454, 34526433, 33994402, 34176852, 20538126, 25461735, 27784735)
Ambry Genetics	RCV002399519	SCV002710381	pathogenic	Cardiovascular phenotype	2024-03-19	criteria provided, single submitter	clinical testing	The c.1783C>T (p.R595W) alteration is located in coding exon 12 of the LDLR gene. This alteration results from a C to T substitution at nucleotide position 1783, causing the arginine (R) at amino acid position 595 to be replaced by a tryptophan (W). Based on data from gnomAD, the T allele has an overall frequency of 0.001% (2/282862) total alleles studied. The highest observed frequency was 0.002% (2/129168) of European (non-Finnish) alleles. This variant has been reported in several individuals with familial hypercholesterolemia (FH) from varying ethnic backgrounds (Descamps, 2001; Damgaard, 2005; Tejedor, 2005; Fouchier, 2005; Chiou, 2010; Jannes, 2015; Bañares, 2017; Pirillo, 2017; Pek, 2018). Another alteration at the same codon, p.R595Q (c.1784G>A), has also been detected in individuals with FH (Fouchier, 2005). This amino acid position is highly conserved in available vertebrate species. Functional studies of this variant demonstrated reduced binding capacity and receptor recycling (Guo, 2019). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.
Fulgent Genetics, Fulgent Genetics	RCV000237585	SCV002789296	pathogenic	Hypercholesterolemia, familial, 1	2021-10-07	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000237585	SCV003827169	pathogenic	Hypercholesterolemia, familial, 1	2022-07-27	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	RCV000237585	SCV004804728	pathogenic	Hypercholesterolemia, familial, 1	2024-03-17	criteria provided, single submitter	research
All of Us Research Program, National Institutes of Health	RCV000237585	SCV004822501	pathogenic	Hypercholesterolemia, familial, 1	2024-01-09	criteria provided, single submitter	clinical testing	This missense variant (also known as p.Arg574Trp in the mature protein) replaces arginine with tryptophan at codon 595 in the fifth LDLR type B repeat of the EGF precursor homology 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). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in over 20 individuals affected with familial hypercholesterolemia (PMID: 11737238, 16250003, 20538126, 25461735, 28502510, 32044282, 32331935, 34037665, 34176852; Color internal data), including three homozygous individuals with severe phenotype (PMID: 27784735). This variant has been identified in 2/282862 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different missense variants occurring at the same codon (p.Arg595Leu and Arg595Gln) have been reported in individuals affected with familial hypercholesterolemia (ClinVar variation ID: 252029, 183126), suggesting that arginine at this position is a functionally and clinically important residue. Based on the available evidence, this variant is classified as Pathogenic.
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	RCV000588105	SCV005045752	pathogenic	Familial hypercholesterolemia	2021-05-12	criteria provided, single submitter	clinical testing	The c.1783C>T (p.Arg595Trp) variant, also known as p.Arg574Trp in LDLR gene that encodes for low density lipoprotein receptor, has been identified in several unrelated individuals (>10) who fulfill the clinical criteria of familial hypercholesterolemia and segregated with disease in ten informative meioses (PMID:11737238, 16250003, 20538126, 25461735, 28502510). In-silico computational prediction tools suggest that the p.Arg595Trp variant may have deleterious effect on the protein function (REVEL score: 0.89). This variant is found to be rare (2/282862 chromosomes) in the general population database, gnomAD. This variant is interpreted as pathogenic by multiple submitters in the ClinVar database including the ClinGen expert panel (ClinVar ID: 161290). Another amino acid substitution at same position (p.Arg595Gln) has been classified as pathogenic by the ClinGen expert panel (ClinVar ID:183126). Therefore, the c.1783C>T (p.Arg595Trp) variant in LDLR gene is classified as pathogenic.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV000237585	SCV005399577	pathogenic	Hypercholesterolemia, familial, 1	2023-07-17	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with familial hypercholesterolaemia 1 (FH; MIM#143890). (I) 0108 - This gene is associated with both recessive and dominant disease. Variants have been reported in heterozygous, compound heterozygous and homozygous states with the recessive disease being more severe (OMIM, PMID: 10978268). (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 24404629). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to tryptophan. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2 & v3) <0.01 (5 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (11 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated low density lipoprotein receptor class B domain (DECIPHER). (I) 0701 - Other missense variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Two alternative missense variants at the same position have been classified as pathogenic or likely pathogenic by an expert panel in ClinVar. (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogneic by an expert panel in ClinVar. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Juno Genomics, Hangzhou Juno Genomics, Inc	RCV000237585	SCV005417069	pathogenic	Hypercholesterolemia, familial, 1		criteria provided, single submitter	clinical testing	PM2_Supporting+PP3_Moderate+PM5+PS4+PP4
CSER _CC_NCGL, University of Washington	RCV002051683	SCV000190312	uncertain significance	Hypercholesterolemia	2014-06-01	no assertion criteria provided	research
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	RCV000237585	SCV000606512	pathogenic	Hypercholesterolemia, familial, 1		no assertion criteria provided	research
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas	RCV000237585	SCV004041644	pathogenic	Hypercholesterolemia, familial, 1	2023-10-09	no assertion criteria provided	clinical testing