Submissions for variant NM_000527.5(LDLR):c.313+2T>C

gnomAD frequency: 0.00001  dbSNP: rs793888517

Total submissions: 20

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	RCV000172957	SCV002506367	pathogenic	Hypercholesterolemia, familial, 1	2022-02-14	reviewed by expert panel	curation	The NM_000527.5(LDLR):c.313+2T>C variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes PM2, PS3_moderate, PVS1_strong, PP1_moderate, PS4, PM3, PP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: PM2 - PopMax MAF = 0.00002941 (0.002941%) in European (non-Finnish) exomes (gnomAD v3.1.2), so PM2 is Met. PS3_moderate - Level 2 assays: PMID 19026292: Homozygous patient cells, 125I-LDL assays - result - 10% LDLR activity. ---- functional study is consistent with damaging effect, so PS3_Moderate is Met. PVS1_strong - Variant is in +2 intronic position, but there are no studies on effect predicted, so give PVS1_Strong to be conservative. PP1_moderate - Variant segregates with FH phenotype in 4 informative meiosis from 2 families: 2 relatives with the phenotype and the variant from Robarts Research Institute, and 2 affected family members with the variant from Germany (PMID: 26036859), so PP1_Moderate is Met. PS4 - Variant meets PM2 and is identified in 19 unrelated index cases from different labs (4 index cases with DLCN>6 from Robarts Research Institute; 4 index cases with DLCN>6 from Color Health, Inc; 1 index case who fulfills the following criteria for FH: i) total cholesterol >= 9.5 mmol/l, ii) triglycerides < 2 mmol/l, iii) presence of tendon xanthomas; or iv) occurrence of hypercholesterolemia or early onset of coronary artery disease in first degree relatives, from The Netherlands (PMID: 7616128); 3 index cases with DLCN>6 (LDL between 7,98 - 9,50 mmol/l and hypercholesterolemia in 1st degree relative) from Germany (PMID: 11462246); 1 index case who fulfills the following criteria for FH: (1) LDL > 95th percentile and triglycerides below 2 mmol/l, and (2) the presence of xanthoma or CHD in the proband or 1st degree relative with type IIa hypercholesterolemia, xanthoma, or CVD, from France (PMID: 12436241); 1 index case with SB criteria for FH (Total cholesterol >290 mg/dL and LDL >200 mg/dL and severe hypercholesterolemia in 1st degree relatives), from Germany (PMID: 14974088); 1 index case with definite FH according to SB criteria from Northern Ireland (PMID: 16159606); 3 index cases fulfilling the following criteria for FH: i) total cholesterol > 8.0 mmol/l and LDL > 6 mmol/l; (ii) premature coronary or vascular disease, or a family history of cardiovascular disorder; and (iii) the presence of tendon xanthoma, from Denmark (PMID: 16542394); 1 index case with definite FH according to SB criteria (total cholesterol = 658 mg/dl and presence of xanthomas, and primary hypercholesterolemia in the probands’ parents or 1st degree relatives), from USA (PMID: 19026292)), so PS4 is Met. PM3 - Variant meets PM2 and is identified in a true homozygous with total cholesterol = 658 mg/dl (PMID: 19026292), so PM3 is Met. PP4 - Variant meets PM2 and is identified in 19 unrelated index cases from different labs as described, so PP4 is Met.
Institute for Integrative and Experimental Genomics, University of Luebeck	RCV000172957	SCV000212132	likely benign	Hypercholesterolemia, familial, 1		criteria provided, single submitter	research
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000844755	SCV000271390	pathogenic	Homozygous familial hypercholesterolemia	2017-10-02	criteria provided, single submitter	clinical testing	The c.313+2T>C variant in LDLR has been reported in 10 individuals with familial hypercholesterolemia (Lombardi 1995, Nauck 2001, Amsellem 2002, Graham 2005, Br usgaard 2006, Braenne 2015). This variant reportedly did not segregate with elev ated LDL cholesterol levels in 2 relatives from 1 family although the authors li st a second variant in both affected family members (Braenne 2015). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 189296) and was absent from large population studies. The c.313+2T>C variant occ urs in the invariant region (+/- 1,2) of the splice consensus sequence and is pr edicted to cause altered splicing leading to an abnormal or absent protein. Hete rozygous loss of LDLR function is an established disease mechanism in familial h ypercholesterolemia. Of note, 2 other prevalent, pathogenic variants have been reported in association with FH at this splice site (c.313+1G>A and c.313+1G>C) in our laboratory, supporting pathogenicity of the c.313+2T>C variant. In summar y, this variant meets criteria to be classified as pathogenic for familial hyper cholesterolemia in an autosomal dominant manner based upon the predicted impact to the protein, presence in multiple affected individuals and absence from the g eneral population.
LDLR-LOVD, British Heart Foundation	RCV000172957	SCV000294609	likely pathogenic	Hypercholesterolemia, familial, 1	2016-03-25	criteria provided, single submitter	literature only
Robarts Research Institute, Western University	RCV000172957	SCV000484778	likely pathogenic	Hypercholesterolemia, familial, 1		criteria provided, single submitter	clinical testing
Invitae	RCV000771312	SCV000544667	pathogenic	Familial hypercholesterolemia	2023-12-26	criteria provided, single submitter	clinical testing	This sequence change affects a donor splice site in intron 3 of the LDLR gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in LDLR are known to be pathogenic (PMID: 20809525, 28645073). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with familial hypercholesterolemia (PMID: 7616128, 11462246, 14974088, 16542394, 21475731). ClinVar contains an entry for this variant (Variation ID: 189296). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	RCV000172957	SCV000583658	pathogenic	Hypercholesterolemia, familial, 1	2017-03-30	criteria provided, single submitter	clinical testing
Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	RCV000172957	SCV000599325	pathogenic	Hypercholesterolemia, familial, 1	2016-03-01	criteria provided, single submitter	curation
GeneDx	RCV000599492	SCV000709932	pathogenic	not provided	2021-12-03	criteria provided, single submitter	clinical testing	Deletions involving coding exons in this gene are frequently reported as pathogenic, regardless of frame prediction (Stenson et al., 2014); Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; Reported as pathogenic or likely pathogenic in ClinVar by other clinical laboratories (ClinVar Variant ID# 189296; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 22390909, 25525159, 14974088, 11462246, 12436241, 15199436, 16159606, 16542394, 26036859, 23936638, 21475731, 21935675, 15556092, 31447099, 32041611, 33303402, 32770674, 33740630, 34037665, 28008010, 7616128)
Color Diagnostics, LLC DBA Color Health	RCV000771312	SCV000903568	pathogenic	Familial hypercholesterolemia	2023-09-08	criteria provided, single submitter	clinical testing	This variant changes a single nucleotide in the intron 3 canonical splice donor site of the LDLR gene and is predicted to cause aberrant splicing. Although RNA studies have not been performed for this variant, other variants affecting the same splice donor site have been shown to cause skipping of exon 3, resulting in an in-frame deletion of part of the ligand binding domain of the LDLR protein (PMID: 27821657). Functional studies in a homozygous patient fibroblast culture showed 10% LDLR activity compared to wild type cells (PMID: 19026292). This variant has been reported in numerous individuals affected with familial hypercholesterolemia (PMID: 7616128, 11462246, 14974088, 16542394, 19026292, 21475731, 28008010, 37119068). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of LDLR function is a known mechanism of disease. Based on available evidence, this variant is classified as Pathogenic.
Mendelics	RCV000172957	SCV001140980	pathogenic	Hypercholesterolemia, familial, 1	2023-03-30	criteria provided, single submitter	clinical testing
Institute of Human Genetics, University of Leipzig Medical Center	RCV000172957	SCV001429294	pathogenic	Hypercholesterolemia, familial, 1	2022-05-25	criteria provided, single submitter	clinical testing	_x000D_ Criteria applied: PVS1_STR, PS4, PS3_MOD, PM3, PP1_MOD, PM2_SUP, PP4
Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	RCV000172957	SCV001432645	pathogenic	Hypercholesterolemia, familial, 1	2019-05-10	criteria provided, single submitter	research
Baylor Genetics	RCV000172957	SCV001521539	pathogenic	Hypercholesterolemia, familial, 1	2020-10-15	criteria provided, single submitter	clinical testing	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
CeGaT Center for Human Genetics Tuebingen	RCV000599492	SCV001747204	likely pathogenic	not provided	2024-01-01	criteria provided, single submitter	clinical testing	LDLR: PVS1:Strong, PM2, PS4:Moderate
Ambry Genetics	RCV002321678	SCV002607541	pathogenic	Cardiovascular phenotype	2022-01-14	criteria provided, single submitter	clinical testing	The c.313+2T>C intronic pathogenic mutation results from a T to C substitution two nucleotides after coding exon 3 in the LDLR gene. This alteration has been reported in association with familial hypercholesterolemia (Lombardi P, J. Lipid Res. 1995 Apr; 36(4):860-7; Dedoussis GV, Hum. Mutat. 2004 Mar; 23(3):285-6; Graham CA, Atherosclerosis 2005 Oct; 182(2):331-40; Huijgen R, Eur. Heart J. 2012 Sep; 33(18):2325-30). This alteration was also reported in a homozygous state in an Indian female with a total cholesterol level of 658 mg/dl (Kolansky DM, Am. J. Cardiol. 2008 Dec; 102(11):1438-43). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation.
Revvity Omics, Revvity	RCV000172957	SCV003827728	pathogenic	Hypercholesterolemia, familial, 1	2022-05-31	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000771312	SCV003922712	pathogenic	Familial hypercholesterolemia	2023-03-07	criteria provided, single submitter	clinical testing	Variant summary: LDLR c.313+2T>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5 splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 251436 control chromosomes (gnomAD). c.313+2T>C has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia (FH), including at least one homozygote (Brusgaard_2006, Kolansky_2008, Kusters_2011). In addition, Kusters_2011 reported this variant was one of most prevalent FH gene mutations and 6.4% of total FH subjects. These data indicate that the variant is very likely to be associated with disease. Kolansky_2008 showed this variant results in 10% LDLR activity of WT in skin fibroblast culture from one homozygous patient. 15 ClinVar submitters (evaluation after 2014) cite this variant as pathogenic (n=13), likely pathogenic (n=1) and benign (n=1), including one expert panel (ClinGen) classified as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	RCV000172957	SCV004171248	pathogenic	Hypercholesterolemia, familial, 1	2023-11-30	criteria provided, single submitter	clinical testing
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	RCV000172957	SCV000606077	pathogenic	Hypercholesterolemia, familial, 1		no assertion criteria provided	research