rs201573863
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 5P and 4B. PP1_StrongBS4PP3
This summary comes from the ClinGen Evidence Repository: NM_000527.5(LDLR):c.2096C>T (p.Pro699Leu) variant is classified as Uncertain significance for Familial Hypercholesterolemia by applying evidence codes (BS4, PP1_Strong and PP3) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1101/2021.03.17.21252755). The supporting evidence is as follows: BS4 - Variant does not segregate with FH phenotype in 11 informative meioses in 6 families (Laboratory of Genetics and Molecular Cardiology).PP1_strong - Variant segregates with FH phenotype in 58 informative meioses in 9 families from Laboratory of Genetics and Molecular Cardiology.PP3 - REVEL: 0,92. LINK:https://erepo.genome.network/evrepo/ui/classification/CA038525/MONDO:0007750/013
Frequency
Consequence
NM_000527.5 missense
Scores
Clinical Significance
Conservation
Publications
- hypercholesterolemia, familial, 1Inheritance: AD, SD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, ClinGen
- homozygous familial hypercholesterolemiaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LDLR | NM_000527.5 | c.2096C>T | p.Pro699Leu | missense_variant | Exon 14 of 18 | ENST00000558518.6 | NP_000518.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.0000920 AC: 14AN: 152140Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000199 AC: 5AN: 251028 AF XY: 0.0000221 show subpopulations
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461566Hom.: 0 Cov.: 35 AF XY: 0.0000179 AC XY: 13AN XY: 727106 show subpopulations
Age Distribution
GnomAD4 genome 0.0000920 AC: 14AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74300 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Hypercholesterolemia, familial, 1 Pathogenic:13Uncertain:4
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Criteria applied: PS4,PP1_STR,PM2,PP3,BS4 -
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The c.2096C>T (p.Pro699Leu) variant, also known as p.Pro678Leu in LDLR gene that encodes for low density lipoprotein receptor, has been identified in numerous unrelated individuals (>25) affected with familial hypercholesterolemia (FH) (PMID: : 21642693, 7489239, 21310417, 26892515, 25461735, 10882754, 22390909, 23375686, 26892515, 27765764, 23064986, 22698793, 27824480, 33994402, 35137788, 11810272, 11851376, 15556092, 16466730, 20506408, 21642693, 23833242, 25461735, 28502495, 29192238, 31106297, 33994402). This variant has been shown to segregate with disease, with 58 informative meioses across 9 families, while it has also shown non-segregation in 11 informative meioses across 6 families (ClinGen review [ClinVar ID: 252219]). This variant has been reported in homozygous state in three individuals affected with severe FH (>13mmol/L) and in compound heterozygous status (along with a LOF variant) in an individual with severe FH (>500mg/dL) (PMID: 25257073, 7489239). In-silico computational prediction tools suggest that the p.Pro699Leu variant may have deleterious effect on the protein function (REVEL score: 0.92). This variant is rare (11/282422 chromosomes) in the general population database, gnomAD. This variant is interpreted as likely pathogenic/pathogenic by several submitters in the ClinVar database (ClinVar ID: 252219). Therefore, the c.2096C>T (p.Pro699Leu) variant in LDLR gene is classified as likely pathogenic. -
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The c.2096C>T (p.Pro699Leu) variant in exon 14 of LDLR gene results in an amino acid change at residue 699 from a proline to a leucine. This variant has been reported in multiple unrelated individuals and families with familial hypercholesterolemia (PMID: 21642693, 7489239, 21310417, 26892515, 25461735, 10882754). Multiple lines of in silico algorithms have predicted this p.Pro699Leu change to be deleterious. Functional studies (PMID: 20089850) demonstrated that the mutant protein misfolded with a loss of normal protein tracking pattern. Therefore, this variant c.2096C>T (p.Pro699Leu) of LDLR is classified as likely pathogenic. -
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The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.004%). Predicted Consequence/Location: Missense variant In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.92; 3Cnet: 0.97). Same nucleotide change resulting in same amino acid change has been previously reported (ClinVar ID: VCV000252219 /PMID: 7489239). A different missense change at the same codon (p.Pro699Ser) has been reported to be associated with LDLR related disorder (ClinVar ID: VCV001934950). Therefore, this variant is classified as VUS according to the recommendation of ACMG/AMP guideline. -
PM2_Supporting+PM5_Supporting+PP3_Moderate+PS4 -
This variant has an overall allele frequency of 0.00004 in the Broad Institute gnomAD Browser (https://gnomad.broadinstitute.org/). In silico analyses indicate this is an evolutionarily conserved residue. This variant has been reported in the literature in multiple individuals and families with familial hypercholesterolemia (Schuster 1995, Thiart 2000, Fouchier 2001, Van Gaal 2001, Huijgen 2011, Tichy 2012, Bertolini 2013, Janness 2015, Sharifi 2016, Wang 2016). Thus, this variant is interpreted as pathogenic. -
NM_000527.5(LDLR):c.2096C>T (p.Pro699Leu) variant is classified as Uncertain significance for Familial Hypercholesterolemia by applying evidence codes (BS4, PP1_Strong and PP3) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1101/2021.03.17.21252755). The supporting evidence is as follows: BS4 - Variant does not segregate with FH phenotype in 11 informative meioses in 6 families (Laboratory of Genetics and Molecular Cardiology). PP1_strong - Variant segregates with FH phenotype in 58 informative meioses in 9 families from Laboratory of Genetics and Molecular Cardiology. PP3 - REVEL: 0,92. -
subject mutated among 2600 FH index cases screened = 1 , family members = 3 with co-segregation / previously described in association with FH/software prediction damaging -
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not provided Pathogenic:4
Reported in the heterozygous state in numerous individuals from different ethnic backgrounds with a clinical diagnosis of FH (PMID: 10882754, 11810272, 11851376, 19318025, 21310417, 21642693, 22698793, 23375686, 24507775, 25461735, 26892515, 31106297, 35339733, 34456049, 35480308); Located in the third EGF-like repeat within the LDL-receptor EGF precursor homology domain (PMID: 12459547, 2988123); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(P678L); This variant is associated with the following publications: (PMID: 11810272, 21310417, 26892515, 10882754, 19318025, 23375686, 22390909, 11851376, 24507775, 21642693, 25461735, 22698793, 34040191, 32719484, 34037665, 33740630, 33303402, 30586733, 32041611, 35339733, 32220565, 23064986, 27824480, 34234266, 27765764, 33994402, 23769672, 31106297, 31447099, 37443404, 20506408, 29192238, 36769882, 12459547, 2988123, 20089850, 34363016, 34456049, 35480308, 28502495, 37409534, 7489239, 25257073, 37967952, 35137788) -
The LDLR c.2096C>T p.Pro699Leu variant, also known as Pro678Leu, (rs201573863) is reported in the literature in several individuals and families with clinically diagnosed familial hypercholesterolemia (selected publications: Ajufo 2021, Brown 2020, Lange 2014, Sun 2018), including a few homozygous or compound heterozygous individuals affected with severe disease (Santos 2014, Schuster 1995). This variant is also reported in ClinVar (Variation ID: 252219), and is found in the general population with an overall allele frequency of 0.0034% (11/282422 alleles) in the Genome Aggregation Database. Computational analyses predict that this variant is deleterious (REVEL: 0.920). Based on available information, this variant is considered to be likely pathogenic. References: Ajufo E et al. A randomized controlled trial of genetic testing and cascade screening in familial hypercholesterolemia. Genet Med. 2021 Sep;23(9):1697-1704. PMID: 34040191. Brown EE et al. Incorporation of genetic testing significantly increases the number of individuals diagnosed with familial hypercholesterolemia. J Clin Lipidol. 2020 May-Jun;14(3):331-338. PMID: 32220565. Lange LA et al. Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol. Am J Hum Genet. 2014 Feb 6;94(2):233-45. PMID: 24507775. Santos RD. What are we able to achieve today for our patients with homozygous familial hypercholesterolaemia, and what are the unmet needs? Atheroscler Suppl. 2014 Sep;15(2):19-25. PMID: 25257073. Schuster H et al. Ten LDL receptor mutants explain one third of familial hypercholesterolemia in a German sample. Arterioscler Thromb Vasc Biol. 1995 Dec;15(12):2176-80. PMID: 7489239. Sun YV et al. Effects of Genetic Variants Associated with Familial Hypercholesterolemia on Low-Density Lipoprotein-Cholesterol Levels and Cardiovascular Outcomes in the Million Veteran Program. Circ Genom Precis Med. 2018 Dec;11(12):e002192. PMID: 31106297. -
The LDLR c.2096C>T (p.Pro699Leu) variant (also known as P678L) has been observed in individuals with low/normal levels of plasma LDL-cholesterol (PMIDs: 21642693 (2011), 20506408 (2010)), and is described as having uncertain significance by the ClinGen FH expert panel (https://erepo.clinicalgenome.org/). However, this variant has been reported and is statistically more frequent in individuals affected with familial hypercholesterolemia (FH) than in the general population and/or healthy controls (PMIDs: 35480308 (2022), 35339733 (2022), 28502495 (2017), 27824480 (2017), 26892515 (2016), 25461735 (2015), 23375686 (2013), 23064986 (2012), 22698793 (2012), 11810272 (2001)). This variant in the homozygous and compound heterozygous state has also been reported in individuals with severe FH (PMIDs: 25257073 (2014), 7489239 (1995)). An experimental study indicated this variant is associated with LDLR protein misfolding and retention (PMID: 20089850 (2010)). The frequency of this variant in the general population, 0.00036 (9/24958 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with 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. -
BS4, PP1, PP3, PM3, PS4 -
Familial hypercholesterolemia Pathogenic:3
This missense variant replaces proline with leucine at codon 699 in the EGF-like repeat C of the EGF precursor homology domain of the LDLR protein. This variant is also known as p.Pro678Leu in the mature protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. A functional study using transfected HeLa cells has shown that this variant causes LDLR protein misfolding and retention in the endoplasmic reticulum (PMID: 20089850). This variant has been reported in over 20 individuals affected with familial hypercholesterolemia (PMID: 10882754, 11810272, 11851376, 19318025, 21310417, 21642693, 22698793, 23064986, 23375686, 26892515, 27824480, 33994402, 34037665, 35137788, 37967952). While this variant has been shown to segregate with disease, with 58 informative meioses across 9 families, it has also shown non-segregation in 11 informative meioses across 6 families (ClinVar SCV001960938.1). This variant has been identified in 11/282422 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 699 of the LDLR protein (p.Pro699Leu). This variant is present in population databases (rs201573863, gnomAD 0.04%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 7489239, 10882754, 21310417, 21642693, 22390909, 23375686, 25461735, 26892515, 27765764). 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 Pro678Leu. ClinVar contains an entry for this variant (Variation ID: 252219). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt LDLR protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. -
Variant summary: LDLR c.2096C>T (p.Pro699Leu) results in a non-conservative amino acid change located in the EGF-like domain (IPR000742) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2e-05 in 251028 control chromosomes. c.2096C>T has been reported in the literature as a heterozygous genotype in multiple individuals affected with autosomal dominant Familial Hypercholesterolemia (example, Schuster_1995, Huijgen_2012, Bertolini_2013, Jannes_2015, Wang_2016, Tichy_2012, Ahmad_2012, Marco-Benedi_2022, Sharifi_2016) to include at-least one compound heterozygous proband with severe Hypercholesterolemia whose obligate carrier father with this variant was reportedly unaffected, i.e., normal cholesterol levels at age 39 (Schuster_1995). This same study also reported co-segregation with Hypercholesterolemia in a second family but did not provide primary evidence supporting this finding (Schuster_1995). As the variant allele was transmitted much more often than the reference allele to affected members in tested families, these data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 23064986, 23375686, 22698793, 22390909, 25461735, Wang_2016 has NO_PMID, 7489239, 34456049, 26892515). Multiple submitters including an expert panel (ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel) have cited clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments but a predominant consensus as Pathogenic/Likely pathogenic (n=12) and VUS (n=4 to include the Expert Panel). Some submitters cite overlapping evidence utilized in the context of this evaluation while the Expert Panel cites both apparent non-segregation and co-segregation without providing primary evidence for independent corroboration. Based on the evidence outlined above, the variant was classified as pathogenic. -
Homozygous familial hypercholesterolemia Pathogenic:1
The p.Pro699Leu variant in LDLR (also reported as p.Pro678Leu in the literature) has been reported in the heterozygous state at least 11 individuals with familial hypercholesterolemia (FH) and 7 individuals with suspected FH (Thiart 2000, Fouchier 2001, Van Gaal 2001, Huijgen 2011, Tichy 2012, Bertolini 2013, Jannes 2015, Wang 2016, Sharif 2016). It was also identified in 1 individual with homozygous FH who had a second pathogenic loss of function variant in LDLR (Schuster 1995). This variant was also present in this individual's father who had normal cholesterol levels, suggesting reduced penetrance. The p.Pro699Leu variant has been reported by other clinical laboratories in ClinVar (Variation ID# 252219) and has been identified in 9/24032 African chromosomes by the Genome Aggregation Database (GnomAD, http://gnomad.broadinstitute.org; dbSNP rs201573863). This frequency is low enough to be consistent with the frequency of FH in the general population. Computational prediction tools and conservation analysis suggest that the p.Pro699Leu variant may impact the protein. In summary, although additional studies are required to fully establish its clinical significance, the p.Pro699Leu variant is likely pathogenic. The ACMG/AMP Criteria applied (Richards 2015): PS4, PM2_supporting, PP3. -
Dyslipidemia Pathogenic:1
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Cardiovascular phenotype Pathogenic:1
The c.2096C>T (p.P699L) alteration is located in exon 14 (coding exon 14) of the LDLR gene. This alteration results from a C to T substitution at nucleotide position 2096, causing the proline (P) at amino acid position 699 to be replaced by a leucine (L). Based on data from gnomAD, the T allele has an overall frequency of <0.01% (11/282422) total alleles studied. The highest observed frequency was 0.04% (9/24958) of African alleles. This variant, also known as p.P678L, has been reported in numerous familial hypercholesterolemia (FH) cohorts, though clinical details were limited in many of the studies (Thiart, 2000; Ahmad, 2012; Sharifi, 2016; Jannes, 2015; Wang, 2016; Gabová, 2017; Kawame, 2021). This alteration has also been described in the compound heterozygous or homozygous state in multiple probands with homozygous FH (Schuster, 1995; Santos, 2014). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at