19-11102788-T-C

Position:

• chr19-11102788-T-C

Variant summary

Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PP4 PS3_Moderate PM3 PS4 PVS1_Strong PP1_Moderate PM2

This summary comes from the ClinGen Evidence Repository: 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. LINK:https://erepo.genome.network/evrepo/ui/classification/CA023690/MONDO:0007750/013

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: LDLR NM_000527.5 splice_donor, intron
• Scores: Splicing: ADA: 0.9880
• Clinical Significance: Pathogenic reviewed by expert panel P:22 B:1
• Conservation: PhyloP100: 5.04

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 17 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• 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.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: 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.313+2T>C		splice_donor_variant, intron_variant		ENST00000558518.6	NP_000518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LDLR	ENST00000558518.6	c.313+2T>C		splice_donor_variant, intron_variant		1	NM_000527.5	ENSP00000454071.1

Frequencies

GnomAD3 genomes AF: 0.0000132 AC: 2 AN: 152084 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.0000294

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1460906 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 726762

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: 0.00000360

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000132 AC: 2 AN: 152084 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 74288

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000113

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:22 Benign:1

Revision: reviewed by expert panel

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:14 Benign:1

Pathogenic, criteria provided, single submitter	research	Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	May 10, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	May 25, 2022	_x000D_ Criteria applied: PVS1_STR, PS4, PS3_MOD, PM3, PP1_MOD, PM2_SUP, PP4 -
Likely benign, criteria provided, single submitter	research	Institute for Integrative and Experimental Genomics, University of Luebeck	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	May 31, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	Mar 30, 2017	- -
Pathogenic, criteria provided, single submitter	curation;literature only	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	Mar 01, 2016	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Robarts Research Institute, Western University	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Nov 30, 2023	- -
Pathogenic, no assertion criteria provided	research	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jan 18, 2024	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 15, 2020	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
Likely pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Juno Genomics, Hangzhou Juno Genomics, Inc	-	PM2_Supporting+PVS1_Strong+PS3_Moderate+PS4+PP4 -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	Mar 30, 2023	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	Feb 14, 2022	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. -

not provided Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2024	LDLR: PVS1:Strong, PM2, PS4:Moderate -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 03, 2021	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) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jul 17, 2023	PP1, PP4, PM2, PM3, PS3_moderate, PS4, PVS1_strong -

Familial hypercholesterolemia Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 26, 2023	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 07, 2023	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Sep 08, 2023	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. -

Homozygous familial hypercholesterolemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Oct 02, 2017

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. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 14, 2022

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Benign	-0.16
CADD	Uncertain	26
DANN	Benign	0.96
Eigen	Pathogenic	0.81
Eigen_PC	Uncertain	0.57
FATHMM_MKL	Uncertain	0.97	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.99
dbscSNV1_RF	Benign	0.67
SpliceAI score (max)		0.97		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.22		Position offset: 2
DS_DL_spliceai		0.97		Position offset: -2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs793888517; hg19: chr19-11213464;