ClinVar Miner

Submissions for variant NM_000527.5(LDLR):c.1285G>A (p.Val429Met)

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Total submissions: 31
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel RCV000003882 SCV005375284 pathogenic Hypercholesterolemia, familial, 1 2023-03-27 reviewed by expert panel curation The NM_000527.5(LDLR):c.1285G>A (p.Val429Met) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying ACMG/AMP evidence codes PS4, PM2, PS3_Moderate, PP3 and PP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (specification version 1.2) on 27 March 2023. The supporting evidence is as follows: PM2: PopMax MAF = 0.00003266 (0.003%) in South Asian exomes (gnomAD v2.1.1). PP3: REVEL = 0.809. PS3_Moderate: Level 2 assay – PMID 2569482 (Leitersdorf et al., 1989) - Immunoprecipitation assay on heterozygous CHO cells where the receptor was degraded more rapidly. After 6 h, only 13% of the LDL receptor protein remained. Level 2 assay – PMID 3202825 (Fourie et al., 1988) - 125I-labelled LDL assay on homozygous patient's fibroblasts with overall LDL receptor activity of ~2% of wildtype. PS4, PP4: Variant meets PM2 and is identified in at least 55 unrelated index cases who fulfill criteria for FH - 1 case with DLCN score >=6 from Genomics Medicine Unit, Navarrabiomed - idiSNA, Spain; - 4 cases with DLCN score >=6 from Robarts Research Institute, Canada; - 9 cases with DLCN score >=6 from Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA, Australia; - 2 cases with DLCN score >=6 and 1 case with possible FH by Simon Broome criteria from Service de Biochimie et de Biologie Moléculaire, Hospices Civils de Lyon, France; - 2 cases with possible FH by Simon Broome criteria from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation), Czech Republic; - 36 cases fulfilling MEDPED criteria from PMID 8399083 (Kotze et al., 1993), South Africa. PP1_Strong: Variant segregates with FH phenotype in 27 informative meiosis from at least 10 families from different labs (Genomics Medicine Unit, Navarrabiomed - idiSNA, Spain; Robarts Research Institute, Canada; Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA, Australia; Service de Biochimie et de Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France; Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Czech Republic; Laboratory of Genetics and Molecular Cardiology, Brazil; PMID 26036859 (Brænne et al., 2016), Germany; PMID 21925660 (Versmissen et al., 2011), the Netherlands): 19 affected family members have the variant and 8 unaffected family members do not have the variant.
Institute for Integrative and Experimental Genomics, University of Luebeck RCV000003882 SCV000212137 likely pathogenic Hypercholesterolemia, familial, 1 criteria provided, single submitter research
LDLR-LOVD, British Heart Foundation RCV000003882 SCV000295341 likely pathogenic Hypercholesterolemia, familial, 1 2016-03-25 criteria provided, single submitter literature only
Robarts Research Institute, Western University RCV000003882 SCV000484726 likely pathogenic Hypercholesterolemia, familial, 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 RCV000003882 SCV000503327 likely pathogenic Hypercholesterolemia, familial, 1 2016-12-16 criteria provided, single submitter clinical testing subjects mutated among 2600 FH index cases screened = 12 , family members = 6 with co-segregation / FH-Afrikaner-2, < 2% LDLR Activity / Software predictions: Conflicting
Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation RCV000003882 SCV000540808 likely pathogenic Hypercholesterolemia, familial, 1 2016-11-05 criteria provided, single submitter clinical testing
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille RCV000003882 SCV000583816 pathogenic Hypercholesterolemia, familial, 1 2017-03-30 criteria provided, single submitter clinical testing
Laboratory of Genetics and Molecular Cardiology, University of São Paulo RCV000003882 SCV000588571 pathogenic Hypercholesterolemia, familial, 1 2016-03-01 criteria provided, single submitter research
Fundacion Hipercolesterolemia Familiar RCV000003882 SCV000607578 pathogenic Hypercholesterolemia, familial, 1 2016-03-01 criteria provided, single submitter research
Labcorp Genetics (formerly Invitae), Labcorp RCV000775062 SCV000627017 pathogenic Familial hypercholesterolemia 2023-11-24 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 429 of the LDLR protein (p.Val429Met). This variant is present in population databases (rs28942078, gnomAD 0.003%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 2569482, 11139254, 11196104, 11668627, 15256764, 19837725, 21475731, 21925660, 23375686). It has also been observed to segregate with disease in related individuals. This variant is also known as p.Val408Met. ClinVar contains an entry for this variant (Variation ID: 3694). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt LDLR protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects LDLR function (PMID: 2569482). For these reasons, this variant has been classified as Pathogenic.
Iberoamerican FH Network RCV000003882 SCV000748052 pathogenic Hypercholesterolemia, familial, 1 2016-03-01 criteria provided, single submitter research
Fulgent Genetics, Fulgent Genetics RCV000003882 SCV000894174 pathogenic Hypercholesterolemia, familial, 1 2018-10-31 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000775062 SCV000909163 pathogenic Familial hypercholesterolemia 2023-08-02 criteria provided, single submitter clinical testing This missense variant replaces valine with methionine at codon 429 of the LDLR protein. This variant is also known as p.Val408Met in the mature protein and as FH Afrikaner-2. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that the mutant protein shows <2% LDLR activity (PMID: 6324732, 1301956, 2569482, 3202825,). This variant has been reported in individuals affected with familial hypercholesterolemia (PMID: 1301956, 1952806, 7649549, 8478013, 9763532, 6324732, 7903269, 19837725, 20506408, 21722902, 23375686, 26036859, 2569482, 6324732, 8478013). It has been shown that this variant segregates with disease in multiple families (PMID: 2569482, 6324732, 8478013). This variant has been identified in 3/251284 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000786355 SCV001134247 pathogenic not provided 2023-10-20 criteria provided, single submitter clinical testing The LDLR c.1285G>A (p.Val429Met) variant has been reported in the published literature in multiple affected individuals and families with heterozygous and homozygous Familial Hypercholesterolemia (PMIDs: 36991406 (2023), 34456049 (2022), 32041611 (2020), 26036859 (2016), 23375686 (2013), 21925660 (2011), 21475731 (2011), 19837725 (2010), 15256764 (2004), 9763532 (1998), and 8478013 (1993)). Experimental studies indicate the variant is damaging to the function of the LDL receptor protein (PMID: 2569482 (1989)). The frequency of this variant in the general population, 0.000012 (3/251284 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000775062 SCV001363968 pathogenic Familial hypercholesterolemia 2022-10-10 criteria provided, single submitter clinical testing Variant summary: LDLR c.1285G>A (p.Val429Met) results in a conservative amino acid change located in the LDLR class B repeat of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251284 control chromosomes. c.1285G>A has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia. These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. This publication reported cells carrying the variant processed the LDL receptor protein more slowly and degraded the protein more rapidly compared to wild-type cells (Leitersdorf_1989). Seventeen clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia RCV000003882 SCV001432624 pathogenic Hypercholesterolemia, familial, 1 2019-05-11 criteria provided, single submitter research
Mayo Clinic Laboratories, Mayo Clinic RCV000786355 SCV001715487 pathogenic not provided 2023-08-04 criteria provided, single submitter clinical testing PP1_strong, PP3, PP4, PM3, PS3_moderate, PS4
GeneDx RCV000786355 SCV001797047 pathogenic not provided 2023-06-07 criteria provided, single submitter clinical testing Described as one of the two founder mutations that account for approximately 80% of FH cases in the Afrikaner population (Kotze et al., 1993); Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate a damaging effect with slower processing of precursor LDLR protein to the mature protein and faster degradation of the protein (Leitersdorf et al., 1989); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Also known as p.(V408M) FH Afrikaner-2; This variant is associated with the following publications: (PMID: 25741868, 20506408, 26036859, 11139254, 22390909, 32759540, 35339733, 21925660, 8478013, 7718024, 9763532, 7903269, 8096412, 1952806, 21475731, 11668627, 11196104, 19837725, 28492532, 15199436, 21722902, 11325764, 7649549, 15256764, 32041611, 33303402, 32719484, 33740630, 33418990, 33599434, 33087929, 8399083, 35379577, 34426522, 30241732, 34037665, 34456049, 23375686, 2569482, 35913489)
CeGaT Center for Human Genetics Tuebingen RCV000786355 SCV002063728 pathogenic not provided 2021-11-01 criteria provided, single submitter clinical testing
3billion RCV000003882 SCV002521638 pathogenic Hypercholesterolemia, familial, 1 2022-05-22 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.001%). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.81; 3Cnet: 0.91). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000003694). A different missense change at the same codon (p.Val429Leu) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000226353, VCV000251767). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
Ambry Genetics RCV002381239 SCV002689385 pathogenic Cardiovascular phenotype 2023-12-20 criteria provided, single submitter clinical testing The c.1285G>A (p.V429M) alteration is located in exon 9 (coding exon 9) of the LDLR gene. This alteration results from a G to A substitution at nucleotide position 1285, causing the valine (V) at amino acid position 429 to be replaced by a methionine (M). Based on data from gnomAD, the A allele has an overall frequency of 0.001% (3/251284) total alleles studied. The highest observed frequency was 0.003% (1/30616) of South Asian alleles. This mutation has been reported in the homozygous and compound heterozygous states in numerous unrelated individuals from various ethnic backgrounds who met strict clinical diagnoses of familial hypercholesterolemia (Leitersdorf, 1989; Bertolini, 2013). In one Dutch study, three independently ascertained probands with this mutation were found to have the same haplotype and subsequently traced back seven generations to a common ancestor, resulting in a kindred of over 160 individuals and more than 10 obligate carriers of this mutation. All family members for whom untreated cholesterol levels were available were reported to have cholesterol levels above the 95th percentile (Sijbrands, 2001; Versmissen, 2011). In one functional study, cultured fibroblasts from an individual homozygous for this mutation exhibited an overall LDL receptor activity of only ~2% of wildtype (Fourie, 1988). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.
Institute of Human Genetics, University Hospital of Duesseldorf RCV000003882 SCV004046803 pathogenic Hypercholesterolemia, familial, 1 criteria provided, single submitter not provided
All of Us Research Program, National Institutes of Health RCV000003882 SCV004820291 pathogenic Hypercholesterolemia, familial, 1 2024-05-06 criteria provided, single submitter clinical testing The c.1285G>A (p.Val429Met) variant (also known as p.Val408Met and FH Afrikaner-2) in the LDLR gene that encodes for low density lipoprotein receptor, has been identified in numerous individuals affected with familial hypercholesterolemia (FH) and segregates with disease in multiple families (PMID: 21925660, 2569482, 23375686, 11196104, 15256764, 21475731). This variant has been reported in the homozygous and compound heterozygous state in numerous unrelated individuals from varied ethnic backgrounds who met strict clinical diagnoses of FH (PMID: 6324732, 1301956, 2569482). Functional studies using patient-derived fibroblasts showed severely reduced LDLR activity (<2%) (PMID: 1301956, 3202825). In-silico computational prediction tools suggest that the p.Val429Met variant may have deleterious effect on the protein function (REVEL score: 0.809). This variant is found to be rare (3/251284 chromosomes; 0.00001194) in the general population database, gnomAD and interpreted as likely pathogenic/pathogenic by multiple submitters in the ClinVar database (ClinVar ID: 3694). Therefore, the c.1285G>A (p.Val429Met) variant in LDLR gene is classified as pathogenic.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV004017225 SCV004847733 pathogenic Homozygous familial hypercholesterolemia 2019-05-04 criteria provided, single submitter clinical testing The p.Val429Met variant in LDLR has been identified in over 25 individuals with familial hypercholesterolemia (FH; including in 2 homozygotes and 3 compound heterozygotes with a known pathogenic variant) and segregated with disease in over 100 affected relatives from at least 1 family (Leitersdorf 1989, Dedoussis 2004, Versmissen 2011). Additionally, this variant was also identified in at least 1 family (of 2 affected sibs) with premature myocardial infraction (MI; Braenne 2015). The p.Val429Met variant has been reported by other clinical laboratories in ClinVar (Variation ID: 3694) and has also been identified in 0.001% (3/251284) of pan-ethnic chromosomes by gnomAD (http://gnomad.broadinstitute.org). This frequency is low enough to be consistent with the frequency of FH in the general population. Computational prediction tools and conservation analysis do not provide strong support for or against an impact to the protein. In vitro functional studies support an impact on protein function (Leitersdorf 1989). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant FH. ACMG/AMP Criteria applied: PS4, PP1_Strong, PM2, PS3_Supporting.
OMIM RCV000003882 SCV000024047 pathogenic Hypercholesterolemia, familial, 1 1993-12-01 no assertion criteria provided literature only
Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital RCV000003882 SCV000268609 pathogenic Hypercholesterolemia, familial, 1 2011-11-07 no assertion criteria provided clinical testing
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum RCV000003882 SCV000606381 pathogenic Hypercholesterolemia, familial, 1 no assertion criteria provided research
Stanford Center for Inherited Cardiovascular Disease, Stanford University RCV000786355 SCV000925141 pathogenic not provided 2017-06-12 no assertion criteria provided provider interpretation p.Val429Met (c.1285G>A; also known as Val408Met or V408M in the literature) in the LDLR gene (NM_000527.4) Given the strong case data for this founder variant, its location in the LDL receptor protein and its rarity in large population databases, we consider this variant disease-causing and we do feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). The variant has been seen in at least 204 unrelated cases of FH (not including this patient's family). There is very strong case data. There are likely many more cases of this variant given that it is a Dutch founder variant. This variant is classified as likely pathogenic or pathogenic by 6 submitters. It was seen in at least 34 individuals submitted by these groups, including 2 individuals from one family. This variant was found in a very large (8-generation, 412-member) Dutch family. 161 members of this family were found to have the variant and high cholesterol levels above the 95th percentile. Furthermore, this group identified a genotype-phenotype correlation: when V408M is maternally transmitted it is associated with a 2-fold increase in mortality risk in untreated individuals with FH. (Versmissen et al 2011). This variant was found in one out of 60 individuals from Ontario, Canada. This patient had Dutch ancestry. This variant was found in 2 of 1070 (of which 52 were homozygotes) Italian individuals with FH (Bertolini et al 2013). This variant was found in 1 Afrikans individual with homozygous FH (of Dutch ancestry), and these authors concluded that the p.Val429Met variant is a Dutch founder variant (Leitersdorf et al. 1989). This variant was identified in 1 of 25 German patients with FH. This variant was found in 4 of 28 individuals of Greek descent, ranging from 34 to 57 years old (Whittal et al 2009). This variant completely abolishes receptor function (Hobbs et al 1992). The valine at codon 429 is almost completely conserved across species, as are neighboring amino acids. Other variants have been reported in association with disease at this codon (p.Val429Leu) nearby codons (p.Asn425Ile, p.Asn425Thrfs, p.Ala431Terfs, p.Ala431Pro, p.Ala431 Thr, p.Leu431Val, p.432Pro, p.Asp433del, p.Asp433Tyr, p.Asp433His). The variant was reported online in 3 of 123,065 individuals in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >140,000 unrelated individuals of African, Asian, European, Ashkenazi, Latino descent. Specifically, the variant was observed in 1 of 15,391 individuals of South Asian descent (MAF=0.0032%), 1 of 12,290 individuals of Latino descent and 1 of 55,800 individuals of European (non-Finnish) descent. 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. 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).
GenomeConnect - Invitae Patient Insights Network RCV000775062 SCV001749524 not provided Familial hypercholesterolemia no assertion provided phenotyping only Variant interpreted as Pathogenic and reported on 06-19-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas RCV000003882 SCV004101084 pathogenic Hypercholesterolemia, familial, 1 2023-11-02 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004745143 SCV005343108 pathogenic LDLR-related disorder 2024-05-17 no assertion criteria provided clinical testing The LDLR c.1285G>A variant is predicted to result in the amino acid substitution p.Val429Met. This variant has been reported in multiple individuals with hypercholesterolemia (for examples, see Leitersdorf et al. 1989. PubMed ID: 2569482, reported as p.Val408Met; Versmissen et al. 2011. PubMed ID: 21925660; Meshkov et al. 2021. PubMed ID: 33418990; Sturm et al. 2021. PubMed ID: 34037665, supplementary table 1). This variant is reported in 0.0033% of alleles in individuals of South Asian descent in gnomAD. This variant is interpreted as pathogenic.

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