Submissions for variant NM_000527.5(LDLR):c.190+4A>T

gnomAD frequency: 0.00001  dbSNP: rs769446356

Total submissions: 19

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	RCV000211667	SCV002506352	likely pathogenic	Hypercholesterolemia, familial, 1	2022-02-09	reviewed by expert panel	curation	NM_000527.5(LDLR):c.190+4A>T variant is classified as Likely pathogenic for Familial Hypercholesterolemia by applying evidence codes (PM2, PP4, PS4 and PS3_Moderate) 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 = 0.00020 (0.02%) in East Asian exomes+genomes (gnomAD v2.1.1). PP4 - Variant meets PM2. Variant identified in 11 unrelated index cases (1 case fulfilling Simon-Broome criteria published in PMID: 21418584; 3 cases fulfilling Simon-Broome criteria published in PMID: 20236128; 5 cases with Dutch lipid clinic network >=6 from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA); 1 case with Dutch lipid clinic network >=6 from Robarts Research Institute; 1 case with MedPed definite from Mayo Clinic Atherosclerosis and Lipid Genomics Laboratory. PS3_Moderate - Level 2 assays: PMID 19208450: Heterozygous patient cells, FACS/RT-PCR/Nothern blotting assays - result - 47% low-density lipoprotein particle receptor activity (LDLR activity reported as a mean value of cell-surface LDLR and LDL internalization measurements); aberrant transcript is not confirmed by sequencing (NMD expected) and is 40% of total transcripts. PS4 - Variant meets PM2. Variant identified in 11 unrelated index cases (1 case fulfilling Simon-Broome criteria published in PMID: 21418584; 3 cases fulfilling Simon-Broome criteria published in PMID: 20236128; 5 cases with Dutch lipid clinic network >=6 from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA); 1 case with Dutch lipid clinic network >=6 from Robarts Research Institute; 1 case with MedPed definite from Mayo Clinic Atherosclerosis and Lipid Genomics Laboratory.
LDLR-LOVD, British Heart Foundation	RCV000211667	SCV000294504	uncertain significance	Hypercholesterolemia, familial, 1	2016-03-25	criteria provided, single submitter	literature only
Robarts Research Institute, Western University	RCV000211667	SCV000484775	likely pathogenic	Hypercholesterolemia, familial, 1		criteria provided, single submitter	clinical testing
Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	RCV000211667	SCV000599315	likely pathogenic	Hypercholesterolemia, familial, 1	2016-03-01	criteria provided, single submitter	curation
GeneDx	RCV000523458	SCV000617499	pathogenic	not provided	2022-06-20	criteria provided, single submitter	clinical testing	Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies suggest a damaging effect leading to reduction in LDLR protein (Holla et al., 2009); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 25525159, 26795593, 15199436, 16205024, 21418584, 16250003, 22883975, 25682442, 23680767, 27765764, 24075752, 19208450, 34037665, 32719484, 33740630, 34573395)
Labcorp Genetics (formerly Invitae), Labcorp	RCV000771311	SCV000752427	pathogenic	Familial hypercholesterolemia	2024-01-19	criteria provided, single submitter	clinical testing	This sequence change falls in intron 2 of the LDLR gene. It does not directly change the encoded amino acid sequence of the LDLR protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs769446356, gnomAD 0.02%). This variant has been observed in individuals with familial hypercholesterolemia (PMID: 15199436, 16205024, 16250003, 21418584, 27765764). ClinVar contains an entry for this variant (Variation ID: 225097). Studies have shown that this variant alters LDLR gene expression (PMID: 19208450). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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.
Color Diagnostics, LLC DBA Color Health	RCV000771311	SCV000903567	pathogenic	Familial hypercholesterolemia	2022-09-22	criteria provided, single submitter	clinical testing	This variant causes an A>T nucleotide substitution at the +4 position of intron 2 of the LDLR gene. Splice site prediction tools predict that this variant may have a significant impact on RNA splicing. A functional RNA study has demonstrated that this variant causes aberrant splicing and degradation of the mutant transcript (PMID: 19208450). Lymphocytes from a heterozygous carrier showed that the levels of cell-surface LDLR protein and internalized LDL were decreased by ~40% and ~55%, respectively, compared to normal cells (PMID: 19208450). This variant has been reported in at least fifteen individuals diagnosed with familial hypercholesterolemia (PMID: 16205024, 16250003, 16792510, 21418584, 22883975, 23680767, 24075752, 25682442, 27765764, 31345425). This variant has been identified in 5/281964 chromosomes 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000771311	SCV001361873	pathogenic	Familial hypercholesterolemia	2019-02-06	criteria provided, single submitter	clinical testing	Variant summary: The variant, LDLR c.190+4A>T alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5 splicing donor site. Two predict the variant weakens a 5' donor site. A functional study, Holla_2009, detected aberrant splicing and found the variant to cause a decrease in LDLR at the cell surface (~40% of normal) and internalization (~55% of normal). The variant allele was found at a frequency of 1.8e-05 in 276542 control chromosomes (gnomAD). c.190+4A>T has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia (Al-Khateeb_2011, Fouchier_2005, Taylor_2010, Leren_2004, Punzalan_2005). These data indicate that the variant is very likely to be associated with disease. Four ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant three times as likely pathogenic/pathogenic and once as uncertain significance. Based on the evidence outlined above, the variant was classified as pathogenic.
Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	RCV000211667	SCV001432599	uncertain significance	Hypercholesterolemia, familial, 1	2019-06-05	criteria provided, single submitter	research
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	RCV000771311	SCV001435003	pathogenic	Familial hypercholesterolemia	2019-04-30	criteria provided, single submitter	clinical testing	The c.190+4A>T variant in the LDLR gene in intron 2 is predicted to disrupts splicing resulting in an abnormal mRNA transcript. This variant has been reported in multiple unrelated individuals with familial hypercholesterolemia (PMID: 15199436, 16205024, 21418584, 27765764). Functional studies have shown reduced internalization and cell surface LDLR protein when this variant is present (PMID: 19208450). The c.190+4A>T variant in the LDLR gene is classified as likely pathogenic.
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	RCV000771311	SCV001445925	pathogenic	Familial hypercholesterolemia	2019-09-09	criteria provided, single submitter	clinical testing	This variant has been previously reported as a heterozygous change in patients with familial hypercholesterolemia (PMID: 15199436, 16205024, 16250003, 21418584, 27765764). Functional studies conducted in EBV-transformed lymphocytes demonstrated that this variant leads to reduced LDLR transcript levels, reduced LDLR protein present at the cell surface, and reduced levels of internalized LDL (PMID: 19208450). This variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.002% (5/276382) and thus is presumed to be rare. Multiple splice prediction tools suggest this variant is likely to interfere with normal splicing. Based on the available evidence, the c.190+4A>T variant is classified as Pathogenic.
AiLife Diagnostics, AiLife Diagnostics	RCV000523458	SCV002503355	uncertain significance	not provided	2020-05-18	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002408912	SCV002721974	likely pathogenic	Cardiovascular phenotype	2024-01-30	criteria provided, single submitter	clinical testing	The c.190+4A>T intronic variant results from an A to T substitution 4 nucleotides downstream of coding exon 2 in the LDLR gene. This alteration was previously detected in Malaysian and Filipino individuals reported to have familial hypercholesterolemia (FH) (Punzalan FE et al. J Atheroscler Thromb. 2005;12(5):276-83; Khateeb A et al. BMC Med Genet. 2011;12:40), and has been detected in other individuals with FH from additional cohorts (Leren TP et al. Semin Vasc Med. 2004;4(1):75-85; Hooper AJ et al. Atherosclerosis. 2012;224(2):430-4; Vandrovcova J et al. Genet Med. 2013;15(12):948-57). One in vitro study indicated this alteration results in reduced LDL receptor activity and possible degradation of mutant transcript (Holla ØL et al. Mol Genet Metab. 2009;96(4):245-52). This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Revvity Omics, Revvity	RCV000211667	SCV003829597	likely pathogenic	Hypercholesterolemia, familial, 1	2022-10-28	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV000211667	SCV004836108	likely pathogenic	Hypercholesterolemia, familial, 1	2023-12-14	criteria provided, single submitter	clinical testing	This variant has been reported in multiple individuals with familial hypercholesterolemia (PMID: 21418584, 20236128, 34573395). It is present in 5 of 281964 total alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/). This variant is predicted to be deleterious by in silico analysis. Well-established functional studies suggest that this variant has a deleterious effect on the protein sufficient to be disease-causing (PMID: 19208450). Different variants at the same splice site motif have been reported in association with disease and are independently classified as likely pathogenic or pathogenic.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV004017496	SCV004848163	likely pathogenic	Homozygous familial hypercholesterolemia	2018-02-08	criteria provided, single submitter	clinical testing	The c.190+4A>T variant in LDLR has been reported in at least 7 individuals with hypercholesterolemia (Fouchier 2005, Punzalan 2005, Al-Khateeb 2011, Vandrovcova 2013, Wang 2016). It has also been identified in 4/18862 East Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs769446356). This variant is located in the 5' splice region, and computational tools do suggest an impact to splicing. In addition, in vitro functional studies provide some evidence that the c.190+4A>T variant may impact protein function (Holla 2009). However, these computational and functional studies may not accurately represent biological function. This variant has been reported in ClinVar (Variation ID: 225097). In summary, although additional studies are required to fully establish its clinical significance, the c.190+4A>T variant is likely pathogenic. ACMG/AMP Criteria applied: PS3_Moderate; PS4_Moderate; PM2; PP3.
Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital	RCV000211667	SCV000268537	pathogenic	Hypercholesterolemia, familial, 1	2010-03-18	no assertion criteria provided	clinical testing
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	RCV000211667	SCV000606036	pathogenic	Hypercholesterolemia, familial, 1		no assertion criteria provided	research
Stanford Center for Inherited Cardiovascular Disease, Stanford University	RCV000523458	SCV000925126	pathogenic	not provided	2016-07-05	no assertion criteria provided	provider interpretation	Intronic variant c.190+4A>T in the LDLR gene (NM_000527.4) Given moderate to strong case data and functional studies showing deleterious impact on the protein, we consider this variant likely pathogenic and we feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). We have seen this variant in a person with FH. Testing was done by Ambry. The variant has been seen in at least 6 unrelated cases of FH (not including this patient's family). There is moderate case data, though no segregation has been demonstrated. The c.190+4A>T variant is listed by Ambry in ClinVar, but without any case data. It was reported in the literature by Khateeb et al., 2011 (1 person with FH), by Punzalan et al., 2005 (3 people with FH), and Vandrovcova et al (1 person with FH). It was also reported in Holla et al., 2009 in a Dutch individual reported to have confirmed FH and in Wald et al., 2015 in a 50 year-old with a total cholesterol level of 294 mg/dL and history of myocardial infarction. No other case data was provided. None of the available studies have performed segregation analysis. Holla et al., 2009 performed some functional studies on the c.190+4A>T variant. Semi-quantitative PCR showed a reduced amount of mRNA transcript from the variant allele compared to control cell lines (less than a 42% cut-off). They did not see exon skipping or activation of a cryptic splice site by RT-PCR or activation of a cryptic splice site by Northern Blot for this variant. They speculated that the mutant transcript containing this variant was degraded. Per the Ambry report, this nucleotide position is well conserved in available vertebrate species. The c.190+4A>T variant was reported online in 2 of 60,098 individuals in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), which currently includes variant calls on ~64,000 individuals of European, African, Latino and Asian descent (as of 4/19/2016). Specifically, the variant was observed in 2 of 4297 East Asian individuals. The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. An allelic c.190+4A>G variant was also listed in ExAC 1 of 60,098 individuals, specifically in 1 of 4297 East Asian individuals. Note that other variants with strong evidence for pathogenicity have been seen at similar frequencies in datasets like this so this does not necessarily rule out pathogenicity (Pan et al 2012). This is especially true for a relatively common disorder like FH.