rs879255206
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PVS1PM2PP4PP1_StrongPS4
This summary comes from the ClinGen Evidence Repository: The NM_000527.5(LDLR):c.2416dup (p.Val806fs) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes PVS1, PP1_Strong, PS4, PM2 and 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: PVS1 - variant is frameshift upstream of amino acid 830, so PVS1 is met.PP1_strong - variant segregates with the FH phenotype in- 1 informative meiosis from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge: 1 relative with the phenotype has the variant;- 7 informative meiosis from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation): data from 4 families: 6 relatives with the phenotype have the variant plus 1 relative without the phenotype does not have the variant;8 informative meiosis support co-segregation, so PP1_Strong is met.PS4 - variant meets PM2 and was identified in - 6 unrelated index cases with DLCN>6 from Roberts Research Institute, Canada;- 1 index case with DLCN>6 from COLOR, USA;- 2 unrelated index cases who fulfill SB criteria of possible FH from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge, Portugal;- 5 unrelated index cases who fulfill SB criteria of possible FH from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation), Czech Republic;14 cases, so PS4 is metPM2 - This variant was not identified in gnomAD (gnomAD v2.1.1), so PM2 is met.PP4 - variant meets PM2 and was identified in 14 unrelated index cases from different labs (please see PS4 for details), so PP4 is met. LINK:https://erepo.genome.network/evrepo/ui/classification/CA040715/MONDO:0007750/013
Frequency
Consequence
NM_000527.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LDLR | NM_000527.5 | c.2416dupG | p.Val806GlyfsTer11 | frameshift_variant | Exon 17 of 18 | ENST00000558518.6 | NP_000518.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251326Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135886
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461762Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727198
GnomAD4 genome
ClinVar
Submissions by phenotype
Hypercholesterolemia, familial, 1 Pathogenic:15Uncertain:1
PVS1, PM2, PP4, PP1_Strong -
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0/188 non-FH alleles -
The mutation leads to the amino acid exchange valine to glycine at position 806 at protein level, as well as a premature termination of protein synthesis.The concomitant loss of LDL receptor activity has already been described in patients with hypercholesterolemia.This variant was observed in a patient with TC up to 360 mg/dl and LDL-C approx. 310 mg/dl. This mutation is therefore classified as pathogenic. PMID: 9767373, 10611908, 25846081 -
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The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.002%). It is predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported to co-segregate with the disease in at least 7 similarly affected relatives/individuals in at least two unrelated families (PMID: 20217239). The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000252330 / PMID: 9767373). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
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subjects mutated among 2600 FH index cases screened = 4 , family members = 2 -
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This variant inserts 1 nucleotide in exon 17 of the LDLR gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in over 20 unrelated heterozygous individuals affected with familial hypercholesterolemia (PMID: 11754108, 22698793, 25461735, 28179607, 28235710, 29213121, 31345425, 33599434, 34037665, 35741760; Color internal data). This variant has also been observed in homozygous state in three individuals affected with severe homozygous familial hypercholesterolemia (PMID: 33599434). It has been shown that this variant segregates with disease in multiple affected individuals across multiple families (PMID: 35741760; ClinVar SCV002568025.1). This variant has been identified in 6/251326 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of LDLR function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
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The NM_000527.5(LDLR):c.2416dup (p.Val806fs) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes PVS1, PP1_Strong, PS4, PM2 and 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: PVS1 - variant is frameshift upstream of amino acid 830, so PVS1 is met. PP1_strong - variant segregates with the FH phenotype in - 1 informative meiosis from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge: 1 relative with the phenotype has the variant; - 7 informative meiosis from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation): data from 4 families: 6 relatives with the phenotype have the variant plus 1 relative without the phenotype does not have the variant; 8 informative meiosis support co-segregation, so PP1_Strong is met. PS4 - variant meets PM2 and was identified in - 6 unrelated index cases with DLCN>6 from Roberts Research Institute, Canada; - 1 index case with DLCN>6 from COLOR, USA; - 2 unrelated index cases who fulfill SB criteria of possible FH from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge, Portugal; - 5 unrelated index cases who fulfill SB criteria of possible FH from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation), Czech Republic; 14 cases, so PS4 is met PM2 - This variant was not identified in gnomAD (gnomAD v2.1.1), so PM2 is met. PP4 - variant meets PM2 and was identified in 14 unrelated index cases from different labs (please see PS4 for details), so PP4 is met. -
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Familial hypercholesterolemia Pathogenic:5
The c.2416dupG (p.Val806Glyfs*11) variant in the LDLR gene is predicted to introduce a premature translational termination codon. This variant has been reported in multiple unrelated individuals affected with familial hypercholesterolemia (PMID 9767373, 10611908, 11754108, 12417285, 20217239) and has shown to segregate with disease in two families (PMID 10611908, 20217239). Therefore, this c.2416dupG (p.Val806Glyfs*11) variant in the LDLR gene is classified as pathogenic. -
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This sequence change creates a premature translational stop signal (p.Val806Glyfs*11) in the LDLR gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LDLR are known to be pathogenic (PMID: 20809525, 28645073). This variant is present in population databases (rs773618064, gnomAD 0.01%). This premature translational stop signal has been observed in individuals with familial hypercholesterolemia (PMID: 9767373, 10611908, 27816806). It has also been observed to segregate with disease in related individuals. Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this LDLR variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 363,995 individuals referred to our laboratory for LDLR testing. This variant is also known as c.785insG, 2412-6insG and c.2416_2417insG (p.Val806Glyfs*10). ClinVar contains an entry for this variant (Variation ID: 252330). For these reasons, this variant has been classified as Pathogenic. -
This variant inserts 1 nucleotide in exon 17 of the LDLR gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in over ten individuals affected with familial hypercholesterolemia (PMID: 11754108, 22698793, 25461735, 28179607, 28235710, 29213121, 31345425). This variant has been identified in 6/246154 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of LDLR function is a known mechanism of disease in familial hypercholesterolemia. Based on available evidence, this variant is classified as Pathogenic. -
Variant summary: The LDLR c.2416dupG (p.Val806GlyfsX11) variant results in a premature termination codon, predicted to cause a truncated or absent LDLR protein due to nonsense mediated decay, which are commonly known mechanisms for disease. This variant was found in 6/246402 control chromosomes (including gnomAD) at a frequency of 0.0000244, which does not exceed the estimated maximal expected allele frequency of a pathogenic LDLR variant (0.0012508). The 6 occurrences observed in gnomAD need to be cautiously considered because the cohort could harbor individuals with an LDLR phenotype. Multiple publications have cited the variant in affected individuals including a large consanguineous Pakistani family that segregated across multiple generations, including one homozygous affected family member with a more severe phenotype (Ajmal_2010). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. -
not provided Pathogenic:4
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This variant alters the translational reading frame of the LDLR mRNA and causes the premature termination of LDLR protein synthesis. This variant has been reported individuals with familial hypercholesterolemia (PMIDs: 27816806 (2016), 10611908 (1999), and 9767373 (1998)). Therefore, this variant is classified as pathogenic. -
Identified in multiple individuals from various ethnic backgrounds with a diagnosis of FH in the published literature (Ekstrm et al., 1998; Nobe et al., 1999; Fouchier et al., 2001; Liguori et al., 2001; Yu et al., 2002; Kuhrov et al., 2002; Miyake et al., 2009; Ajmal et al., 2010; Dukov et al., 2011; Bertolini et al., 2013; Jannes et al., 2015; Khera et al., 2016; Setia et al., 2016; Xiang et al., 2017; Fairoozy et al., 2017; Trinder et al., 2019); Not observed at significant frequency in large population cohorts (gnomAD); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Also known as c.785insG, c.2411insG, and c.2416_2417insG; This variant is associated with the following publications: (PMID: 23375686, 25846081, 11317362, 23535506, 11810272, 29213121, 25461735, 11754108, 10611908, 20217239, 18718593, 27050191, 21310417, 25682442, 28235710, 12417285, 27816806, 28994502, 31491741, 31345425, 32041611, 33303402, 32770674, 34037665, 33740630, 33418990, 33599434, 32331935, 9767373) -
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Homozygous familial hypercholesterolemia Pathogenic:1
The p.Val806Glyfs11 variant in LDLR has been reported in more than 15 individuals with familial hypercholesterolemia (FH; over 10 heterozygotes, 3 homozygotes and 2 compound heterozygotes with other LDLR variants of uncertain significance) and segregated with disease in more than 13 affected relatives in at least 2 families (Ekstrom 1998, Nobe 1999, Fouchier 2001, Kuhrova 2002, Miyake 2009, Ajmal 2010, Tichy 2012, Setia 2016, Fairoozy 2017). It has also been reported by other clinical laboratories in ClinVar (Variation ID: 252330) and has been identified in 0.01% (3/30614) of South Asian chromosomes and 0.002% (3/113724) of 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. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 806 and leads to a premature termination codon 11 amino acids downstream. Additionally, in vitro functional studies support an impact on protein function (Miyake 2009). Loss of function of the LDLR gene is an established disease mechanism in autosomal dominant FH. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant FH. ACMG/AMP Criteria applied: PP1_Strong, PVS1, PS3_Supporting, PS4_Strong. -
LDLR-related disorder Pathogenic:1
The LDLR c.2416dupG variant is predicted to result in a frameshift and premature protein termination (p.Val806Glyfs*11). This variant, also known as p.Val785Glyfs*11, has been reported in several patients with hypercholesterolemia (Kuhrová et al. 2002. PubMed ID: 11754108; Leren et al. 2021. PubMed ID: 33740630. Table S1). This variant is reported in 0.0098% of alleles in individuals of South Asian descent in gnomAD. Frameshift variants in LDLR are expected to be pathogenic, and this variant has been interpreted as pathogenic by the ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel (VCEP, https://www.ncbi.nlm.nih.gov/clinvar/variation/252330/). This variant is interpreted as pathogenic. -
Cardiovascular phenotype Pathogenic:1
The c.2416dupG pathogenic mutation, located in coding exon 17 of the LDLR gene, results from a duplication of G at nucleotide position 2416, causing a translational frameshift with a predicted alternate stop codon (p.V806Gfs*11). This alteration, historically identified as p.V785Gfs*11, has been reported in multiple individuals with familial hypercholesterolemia (FH) (Ekström U et al. Eur. J. Clin. Invest., 1998 Sep;28:740-7; Kuhrová V et al. Hum. Mutat., 2002 Jan;19:80; Bertolini S et al. Atherosclerosis, 2013 Apr;227:342-8; Fan LL et al. Appl. Biochem. Biotechnol., 2015 May;176:101-9; Fairoozy RH et al. Sci Rep, 2017 Dec;7:17087). In addition, co-segregation with FH in a large Pakistani family has been reported (Ajmal M et al. Mol. Biol. Rep., 2010 Dec;37:3869-75). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at