Submissions for variant NM_000527.5(LDLR):c.314-2A>C

gnomAD frequency: 0.00001  dbSNP: rs879254470

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
LDLR-LOVD, British Heart Foundation	RCV000237624	SCV000294616	likely pathogenic	Hypercholesterolemia, familial, 1	2016-03-25	criteria provided, single submitter	literature only
Robarts Research Institute, Western University	RCV000237624	SCV000484777	likely pathogenic	Hypercholesterolemia, familial, 1		criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000775035	SCV000832877	pathogenic	Familial hypercholesterolemia	2024-09-17	criteria provided, single submitter	clinical testing	This sequence change affects an acceptor 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: 27765764, 27824480). This variant is also known as IVS3-2A>C inthe literature. ClinVar contains an entry for this variant (Variation ID: 251142). 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	RCV000775035	SCV000909132	pathogenic	Familial hypercholesterolemia	2024-02-28	criteria provided, single submitter	clinical testing	This variant (also known as IVS3-2A>C) causes an A to C nucleotide substitution at the -2 canonical splice acceptor site of intron 3 of the LDLR gene. Splice site prediction tools suggest that this variant may have a significant impact on RNA splicing. Although this prediction has not been confirmed in published RNA studies, this variant is expected to result in an absent or disrupted protein product. This variant has been reported in over 10 individuals affected with familial hypercholesterolemia (PMID: 11668627, 27765764, 27824480, 32220565, 34037665). 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.
GeneDx	RCV001764224	SCV002000726	pathogenic	not provided	2023-06-18	criteria provided, single submitter	clinical testing	Not observed at significant frequency in large population cohorts (gnomAD); 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.; This variant is associated with the following publications: (PMID: 25525159, 27765764, 31447099, 32041611, 26582918, 32220565, 33303402, 11668627, 34037665)
Ambry Genetics	RCV002321913	SCV002608980	pathogenic	Cardiovascular phenotype	2022-02-16	criteria provided, single submitter	clinical testing	The c.314-2A>C intronic pathogenic mutation results from an A to C substitution two nucleotides upstream from coding exon 4 in the LDLR gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and may result in the creation or strengthening of a novel splice acceptor site. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNAdecay; however, direct evidence is unavailable. The exact functional effect of the altered amino acid sequence is unknown; however, the impacted region is critical for protein function (Ambry internal data). This alteration has been described in familial hypercholesterolemia (FH) cohorts (Wang J et al. Hum Mutat. 2001;18:359; Wang J et al. Arterioscler Thromb Vasc Biol, 2016 12;36:2439-2445; Sturm AC et al. JAMA Cardiol, 2021 08;6:902-909). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Another alteration impacting the same acceptor site (c.314-1G>A) has also been detected in individuals with FH (Huijgen et al 2010; Hum Mut 31(6):752-60; Lombardi P et al. Hum Mutat, 1998;Suppl 1:S172-4; Luirink IK et al. Atherosclerosis, 2019 06;285:87-92). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Revvity Omics, Revvity	RCV000237624	SCV003827817	pathogenic	Hypercholesterolemia, familial, 1	2022-11-08	criteria provided, single submitter	clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV004017541	SCV004848181	likely pathogenic	Homozygous familial hypercholesterolemia	2018-03-21	criteria provided, single submitter	clinical testing	The c.314-2A>C variant in LDLR has been reported in the heterozygous state in at least 5 individuals with familial hypercholesterolemia (FH; Wang 2001, Wang 2016. This variant has also been reported in ClinVar (Variation ID: 251142) and was absent from large population studies. This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and is predicted to cause altered splicing leading to the activation of a downstream splice site that would result in the first 8 bases of the exon to be spliced out, causing a frameshift which alters the protein's amino acid sequence and leads to a premature termination codon 22 amino acids downstream. In summary, although additional studies are required to fully establish its clinical significance, the c.314-2A>C variant is likely pathogenic. ACMG/AMP Criteria applied (Richards 2015): PVS1_Strong; PM2; PS4_Supporting.
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine	RCV000775035	SCV005045755	pathogenic	Familial hypercholesterolemia	2023-10-18	criteria provided, single submitter	clinical testing	The c.314-2A>C intronic variant, also known as IVS3-2A>C is located at the canonical acceptor splice site of intron 3 of the LDLR gene, that encodes for low density lipoprotein receptor. This variant has been reported in at least ten individuals affected with familial hypercholesterolemia (FH) (PMID:11668627, 27765764, 34037665, 32220565). Another intronic variant affecting the same nucleotide, c.314-2A>G, has also been reported in individuals with FH (PMID: 27824480). Variants affecting the same splice site (c.314-1G>A and c.314-3C>T) have been observed in individuals diagnosed with FH (PMID 11810272, 16250003). In-silico computational prediction tools suggest that the c.314-2A>C variant likely leads to acceptor loss (SpliceAI: 0.99 [acceptor loss], 0.32 [acceptor gain at +10bp position]) and disturb normal splicing, resulting in aberrant or absence of protein product (PMID: 16199547). This variant is absent in the general population database, gnomAD. This variant has been interpreted as likely pathogenic/pathogenic by multiple submitters in the ClinVar database (ID: 251142). Therefore, the c.314-2A>C intronic variant in the LDLR gene is classified as pathogenic.
All of Us Research Program, National Institutes of Health	RCV000237624	SCV005426438	pathogenic	Hypercholesterolemia, familial, 1	2024-09-02	criteria provided, single submitter	clinical testing	The c.314-2A>C intronic variant, also known as IVS3-2A>C is located at the canonical acceptor splice site of intron 3 of the LDLR gene, that encodes for low density lipoprotein receptor. This variant has been reported in at least ten individuals affected with familial hypercholesterolemia (FH) (PMID:11668627, 27765764, 34037665, 32220565). Another intronic variant affecting the same nucleotide, c.314-2A>G, has also been reported in individuals with FH (PMID: 27824480). Variants affecting the same splice site (c.314-1G>A and c.314-3C>T) have been observed in individuals diagnosed with FH (PMID 11810272, 16250003). In-silico computational prediction tools suggest that the c.314-2A>C variant likely leads to acceptor loss (SpliceAI: 0.99 [acceptor loss], 0.32 [acceptor gain at +10bp position]) and disturb normal splicing, resulting in aberrant or absence of protein product (PMID: 16199547). This variant is absent in the general population database, gnomAD. This variant has been interpreted as likely pathogenic/pathogenic by multiple submitters in the ClinVar database (ID: 251142). Therefore, the c.314-2A>C intronic variant in the LDLR gene is classified as pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000775035	SCV006070866	pathogenic	Familial hypercholesterolemia	2025-03-03	criteria provided, single submitter	clinical testing	Variant summary: LDLR c.314-2A>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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing and loss of LDLR function. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a canonical 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 249448 control chromosomes. c.314-2A>C has been reported in the literature in individuals affected with Hypercholesterolemia (examples: Sturm_2021, Wang_2001). These data indicate that the variant is likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 34037665, 11668627). ClinVar contains an entry for this variant (Variation ID: 251142). Based on the evidence outlined above, the variant was classified as pathogenic.