ClinVar Miner

Submissions for variant NM_000527.4(LDLR):c.313+1G>A

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Total submissions: 25
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000844753 SCV000271388 pathogenic Homozygous familial hypercholesterolemia 2019-03-26 criteria provided, single submitter clinical testing The c.313+1G>A variant in LDLR has been reported in >140 individuals with familial hypercholesterolemia (FH) and segregated with disease in at least 5 affected relatives from 2 families (Leren 1994, Sun 1995, Lombardi 2000, Hooper 2012). This variant has also been identified in 7/111670 European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This frequency is low enough to be consistent with the frequency of FH in the general population. The c.313+1G>A variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and is predicted to cause altered splicing that would preserve the protein reading frame, leading to an abnormal protein. Furthermore, in vitro functional studies provide some evidence that this variant may impact protein function (Sun 1995, Cameron 2009). In summary, this variant meets criteria to be classified as pathogenic for FH in an autosomal dominant manner based upon presence in multiple affected individuals, segregation studies, low frequency in the general population, and impact to the protein. The ACMG/AMP Criteria applied: PS4, PM2, PP1_Moderate, PVS1_Moderate.
LDLR-LOVD, British Heart Foundation RCV000003934 SCV000294604 likely pathogenic Familial hypercholesterolemia 1 2016-03-25 criteria provided, single submitter literature only
Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge RCV000003934 SCV000322888 pathogenic Familial hypercholesterolemia 1 2016-03-01 criteria provided, single submitter research 0/208 non-FH alleles; 0/100 healthy control individuals
Robarts Research Institute,Western University RCV000003934 SCV000484776 likely pathogenic Familial hypercholesterolemia 1 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 RCV000003934 SCV000503132 likely benign Familial hypercholesterolemia 1 2016-12-16 criteria provided, single submitter clinical testing subjects mutated among 2600 FH index cases screened = 4/FH-Europe
Invitae RCV000791438 SCV000544679 pathogenic Familial hypercholesterolemia 2019-12-30 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 3 of the LDLR gene. It is has been shown to disrupt mRNA splicing and results in an absent or disrupted protein product (PMID: 19361455, 22390909). Truncating variants in LDLR are known to be pathogenic (PMID: 20809525). This particular variant has been shown to segregate with familial hypercholesterolemia (PMID: 7718019) and has been observed in multiple unrelated individuals with hypercholesterolemia (PMID: 22390909, 20045108, 10532689, 14974088) and early-onset myocardial infarction (PMID: 25487149). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000058917 SCV000583373 pathogenic not provided 2019-01-09 criteria provided, single submitter clinical testing The c.313+1 G>A pathogenic variant in the LDLR gene has been previously reported in association with both heterozygous and homozygous FH (Leren et al., 1994; Lombardi et al., 1995; Jensen et al., 1999; Deiana et al., 2000; Lombardi et al., 2000; Dedoussis et al., 2004; Bourbon et al., 2008; Chmara et al., 2010; Romano et al., 2010; Hooper et al., 2012; Huijgen et al., 2012; Ma et al., 2017) as well as early-onset myocardial infarction (Do et al., 2015). This variant has also been described as a founder mutation in the Norwegian population (Leren et al., 1994). In addition, c.313+1 G>A has been identified in other individuals referred for FH genetic testing at GeneDx. Furthermore, the c.313+1 G>A variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). The c.313+1 G>A variant destroys the canonical splice donor site in intron 3 and is predicted to cause abnormal gene splicing. Functional studies by Cameron et al. (1999) demonstrated that c.313+1G>A disrupts mRNA splicing, resulting in a transcript which skips exon 3 and includes intron 3, and producing a receptor with a reduced ability to internalize low density lipoprotein. Multiple other splice site variants in the LDLR gene, including two different pathogenic variants affecting the same nucleotide (c.313+1 G>T, c.313+1 G>C), have been reported in the Human Gene Mutation Database in association with hypercholesterolemia (Stenson et al., 2014).
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille RCV000003934 SCV000583655 pathogenic Familial hypercholesterolemia 1 2017-03-30 criteria provided, single submitter clinical testing
Laboratory of Genetics and Molecular Cardiology, University of São Paulo RCV000003934 SCV000588493 pathogenic Familial hypercholesterolemia 1 2016-03-01 criteria provided, single submitter research
Fundacion Hipercolesterolemia Familiar RCV000003934 SCV000607443 pathogenic Familial hypercholesterolemia 1 2016-03-01 criteria provided, single submitter research
Athena Diagnostics Inc RCV000058917 SCV000614008 pathogenic not provided 2017-06-30 criteria provided, single submitter clinical testing
Iberoamerican FH Network RCV000003934 SCV000748082 pathogenic Familial hypercholesterolemia 1 2016-03-01 criteria provided, single submitter research
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine RCV000003934 SCV000839995 pathogenic Familial hypercholesterolemia 1 2017-08-21 criteria provided, single submitter clinical testing The c.313+1G>A variant in LDLR gene destroys the canonical splice donor site in intron 3 and is predicted to result in abnormal splicing of the LDLR message. Functional studies have shown that the c.313+1G>A variant disrupts mRNA splicing and produces a protein with abnormal function (PMID 19361455). This variant has been reported in multiple unrelated individuals with hypercholesterolemia (PMID 7718019, 22390909, 22883975, 20045108, 20145306, 15523646) and individuals with early-onset myocardial infarction (PMID 25487149). This variant is classified as pathogenic.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000058917 SCV000888166 pathogenic not provided 2018-07-16 criteria provided, single submitter clinical testing
Color RCV000791438 SCV001346458 pathogenic Familial hypercholesterolemia 2018-10-09 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000791438 SCV001372436 pathogenic Familial hypercholesterolemia 2020-06-16 criteria provided, single submitter clinical testing Variant summary: LDLR c.313+1G>A 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: Four predict the variant abolishes a 5 splicing donor site. Experimental evidence supports these predictions indicating that this variant results in two mutant transcripts, one has skipping of exon 3 and the other has inclusion of intron 3 (Cameron_2009, Jensen_1996). The transcript with skipping of exon 3 was demonstrated to have considerably reduced cell-surface LDLR and total amounts of internalized LDL, indicating that the variant LDLR is markedly dysfunctional (Cameron_2009). The variant allele was found at a frequency of 2.8e-05 in 251424 control chromosomes (gnomAD). c.313+1G>A has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia (e.g. Deiana_2000, Jensen_1996, Mozas_2004, Leren_1994). These data indicate that the variant is very likely to be associated with disease. Fourteen ClinVar submitters (evaluation after 2014) cite the variant as pathogenic/likely pathogenic (n=13) and as likely benign (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.
Institute of Human Genetics, University of Leipzig Medical Center RCV000003934 SCV001429402 pathogenic Familial hypercholesterolemia 1 2019-02-05 criteria provided, single submitter clinical testing
Brunham Lab, Centre for Heart and Lung Innovation,University of British Columbia RCV000003934 SCV001432644 pathogenic Familial hypercholesterolemia 1 2019-01-22 criteria provided, single submitter research
OMIM RCV000003934 SCV000024099 pathogenic Familial hypercholesterolemia 1 1996-10-16 no assertion criteria provided literature only
SNPedia RCV000058917 SCV000090438 not provided not provided no assertion provided not provided
Blueprint Genetics RCV000003934 SCV000207022 pathogenic Familial hypercholesterolemia 1 2014-09-25 no assertion criteria provided clinical testing
Cardiovascular Genetics Laboratory,PathWest Laboratory Medicine WA - Fiona Stanley Hospital RCV000003934 SCV000268554 pathogenic Familial hypercholesterolemia 1 2008-06-09 no assertion criteria provided clinical testing
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde,Academisch Medisch Centrum RCV000003934 SCV000606074 pathogenic Familial hypercholesterolemia 1 no assertion criteria provided research
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000003934 SCV000733814 pathogenic Familial hypercholesterolemia 1 no assertion criteria provided clinical testing
Stanford Center for Inherited Cardiovascular Disease, Stanford University RCV000058917 SCV000924843 likely pathogenic not provided 2017-02-09 no assertion criteria provided provider interpretation Genetic testing: The patient had genetic testing for the familial hypercholesterolemia panel. The test included sequencing of three genes associated with familial hypercholesterolemia: LDLR, APOB and PCSK9. Results reported on October 17, 2017 showed that the following variant was identified (see report below): c.313+1G>A in the LDLR gene (NM_000527.4) Ambry classifies this variant as pathogenic. Given sufficient case data and functional in vitro studies, we consider this variant very likely disease causing and we feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). This variant is a common cause of FH around the world. It is referred to as the FH-Elverum allele and the FH-Olbia allele. It's been identified in multiple populations around the world including Austria, Belgium, Denmark, Germany, Italy, Spain, Korea, Norway, The Netherlands, Russia, UK, Sweden, and South Africa (black). It's been identified in up to 25% of Norwegian FH patients and 5% of Western Australian patients. IT has also been reported in a case of homozygous FH. It has been written about in 14 publications and is listed as pathogenic or likely pathogenic by all seven entries in clinvar. An in vitro study found this mutation leads to several alternatively spliced transcripts, one of which skips exon 3 and can result in an abnormal LDLR protein with reduced function (Cameron et al. Clin Chim Acta. 2009. 403(1-2):13-15). This variant is located near a CpG enriched region which may be a mutational hot spot. This variant likely leads to loss of function of the LDL-receptor given its exon skipping nature. There are seven individuals with variation at c.313+1 position listed in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on 126,184 unrelated individuals at this position who are of African, Asian, European, Latino, and Ashkenazi descent. All 7 individuals are of European descent. This corresponds to about 1 in 8,015 European individuals in the general population which confirms that it's likely a common cause of FH in the European populations.

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