rs769370816
Variant summary
Our verdict is Pathogenic. The variant received 15 ACMG points: 15P and 0B. PS4PP1_StrongPM3PS3_SupportingPM2PP3PP4
This summary comes from the ClinGen Evidence Repository: The NM_000527.5(LDLR):c.1618G>A (p.Ala540Thr) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes PS4, PP1_Strong, PM2, PM3, PP3, PP4, PS3_Supporting 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: PS4 - variant meets PM2 and was identified in:- at least 1 index case with DLCN at least 8 (TC =700mg/dl) from Ambry Genetics, USA;- 14 unrelated index cases, all with DLCN >=6 from Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière), France;- at least 5 unrelated index cases (3 with Simon Broome definite FH, 2 with Simon Broome possible FH) from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation), Czech Republic;- 2 unrelated index cases who fulfill SB criteria of possible FH from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge, Portugal;- 4 unrelated index cases, all with DLCN >=6 from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA), Australia;- 2 unrelated index cases, all with Dutch lipid clinic network >=6 from Robarts Research Institute, Canada;- at least 1 index case with DLCN>=6 from PMID 19318025 (Alonso et al., 2009), Spain;- at least 1 index case with SB criteria for FH from PMID 21376320 Chiou et al., 2011), Taiwan,--- 30 cases, so PS4 is metPP1_strong - variant segregates with the FH phenotype in 39 informative meiosis from at least 14 families:- 20 informative meiosis from 7 families from Laboratory of Genetics and Molecular Cardiology, University of São Paulo: 16 relatives with the variant have LDL-C >75th percentile, and 4 relatives without the variant have LDL-C <50th percentile;- 1 informative meiosis from Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière): 1 relative positive for variant had LDL-C >75th percentile;- 8 informative meiosis from 3 families from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation): F1 with 2 relatives positive for variant and having LDL-C >75th percentile, and 2 relatives negative for variant and having LDL-C <50th percentile, F2: 1 relative who was positive for the variant and had LDL-C >75th percentile, F3: 2 relatives who were positive for variant with LDL-C >75th percentile, and 1 relative who was negative for the variant with LDL-C <50th percentile;- 2 informative meiosis from 2 families from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge: 1 relative positive for variant with LDL-C >75th percentile in each family;- 8 informative meiosis (unknown how many families) from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA): 5 relatives positive for variant with LDL-C >75th percentile, and 3 relatives were negative for variant with LDL-C <50th percentile.--- 39 segregations, so PP1_Strong is metPM2 - PopMax MAF = 0.00006533 (0.007%) in South Asian exomes (gnomAD v2.1.1). It is below than 0.02%, so PM2 is met.PM3 - variant meets PM2 and was identified in:- 1 index case homozygous for the variant with TC = 700mg/dl at 7 years old from Ambry Genetics. ---> individual is homozygous for variant and has an homozygous phenotype, so PM3 is met.- 2 unrelated index cases, both homozygous for the variant, with LDL-C 352mg/dL under statin treatment (352/0.7 = 503mg/dl) and LDL-C=409mg/dl under statin treatment (409/0.7 = 584mg/dl), respectively, both from Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière) ---> individuals are homozygous for variant and have an homozygous phenotype, so PM3 is met.PP3 - REVEL = 0.888. It is above 0.75, so PP3 is met.PP4 - variant meets PM2 and was identified in at least 30 unrelated index cases who fulfill clinical FH criteria (see PS4 for details), so PP4 is met.PS3_supporting - Level 3 FS: Sun et al., 1997 (PMID 9409298) - Htz patients' fibroblasts, immunoblot and 125I-LDL assays - results: 40-50% LDLR activity, cell surface LDLR 40-50% LDLR.--- Activity is below 85%, so PS3_Supporting is met. LINK:https://erepo.genome.network/evrepo/ui/classification/CA035437/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: Pathogenic. The variant received 15 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LDLR | NM_000527.5 | c.1618G>A | p.Ala540Thr | missense_variant | Exon 11 of 18 | ENST00000558518.6 | NP_000518.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD2 exomes AF: 0.00000795 AC: 2AN: 251472 AF XY: 0.0000147 show subpopulations
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461164Hom.: 1 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726916 show subpopulations
Age Distribution
GnomAD4 genome
ClinVar
Submissions by phenotype
Hypercholesterolemia, familial, 1 Pathogenic:18
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The variant NM_000527.5:c.1618G>A (chr19:11116125) in LDLR was detected in 11 heterozygotes out of 58K WGS Icelanders (MAF= 0,009%). Following imputation in a set of 166K Icelanders (22 imputed heterozygotes) we observed an association with LDL cholesterol using measurements from 128289 individuals (Effect (SD)= 1.39, P= 3.27e-06) and Non-HDL cholesterol using measurements from 136901 individuals (Effect (SD)= 1.16, P= 1.02e-04). This variant has been reported in ClinVar previously as pathogenic. Based on ACMG criteria (PS4, PM1, PP3, PP5_Strong) this variant classifies as likely pathogenic. -
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The c.1618G>A (p.Ala540Thr) variant identified in the LDLR gene substitutes a well conserved Alanine for Threonine at amino acid 540/861 (exon 11/18). This variant is absent from gnomAD(v3.1.1) suggesting it is not a common benign variant in the populations represented in that database. In silico algorithms predict this variant to be Damaging (SIFT; score:0.001) and Pathogenic (REVEL; score:0.888) to the function of the canonical transcript. This variant is reported as Pathogenic and Likely Pathogenic in ClinVar (VarID:226363), and has been reported in multiple affected individuals in the literature [PMID:11196104, 15241806, 18718593, 21376320, others], includingin some families in which it segregates with disease. Given its presence in multiple affected individuals in the literature, absence in population databases, and in silico prediction of deleterious effect on protein function, the c.1618G>A (p.Ala540Thr) variant identified in the LDLR gene is reported as Likely Pathogenic. -
subjects mutated among 2600 FH index cases screened = 4 (2 homozygotes), family members 1 (1 homozygote) with co-segregation) / previously described in association with FH/Software predictions: Conflicting -
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0/190 non-FH alleles -
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Criteria applied: PS4,PP1_STR,PM2,PS3_SUP -
The c.1618G>A (p.Ala540Thr) variant in the LDLR gene is located on the exon 11 and is predicted to replace alanine with threonine at codon 540 (p.Ala540Thr). This variant has been reported in more than 10 unrelated individuals with familial hypercholesterolemia (FH) (PMID: 35052492, 33807407, 33533259, 28502495, 27680772, 27578104). This variant segregates with FH phenotype in 39 informative meiosis (14 families) from different laboratories according to ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel. Experimental study with heterozygous patient cells proved defective LDLR expression and activity (40-50%) (PMID 9409298). The expert panel has identified homozygous and compound heterozygous conditions of this variant along with a pathogenic variant (p.Cys27Trp) with severe FH phenotype (LDL-C>500mg/dl) (PMID: 23538283). The variant has been reported in ClinVar as pathogenic (ID: 226363). The variant is rare in the general population according to gnomAD (2/251472). Computational prediction algorithms suggest a deleterious impact for this variant (REVEL score 0.888). Therefore, the c.1618G>A (p.Ala540Thr) variant of LDLR has been classified as pathogenic. -
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The c.1618G>A;p.(Ala540Thr) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 226363; PMID: 9544745; 11196104; 15200491; 15241806; 18718593; 21376320; 23375686; 24075752; 25461735; 19007590) - PS4. The variant is present at low allele frequencies population databases (rs769370816 – gnomAD 0.00007953%; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2_supporting. The variant co-segregated with disease in multiple affected family members (PMID: 15241806) - PP1. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is likely pathogenic. -
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The NM_000527.5(LDLR):c.1618G>A (p.Ala540Thr) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes PS4, PP1_Strong, PM2, PM3, PP3, PP4, PS3_Supporting 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: PS4 - variant meets PM2 and was identified in: - at least 1 index case with DLCN at least 8 (TC =700mg/dl) from Ambry Genetics, USA; - 14 unrelated index cases, all with DLCN >=6 from Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière), France; - at least 5 unrelated index cases (3 with Simon Broome definite FH, 2 with Simon Broome possible FH) from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation), Czech Republic; - 2 unrelated index cases who fulfill SB criteria of possible FH from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge, Portugal; - 4 unrelated index cases, all with DLCN >=6 from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA), Australia; - 2 unrelated index cases, all with Dutch lipid clinic network >=6 from Robarts Research Institute, Canada; - at least 1 index case with DLCN>=6 from PMID 19318025 (Alonso et al., 2009), Spain; - at least 1 index case with SB criteria for FH from PMID 21376320 Chiou et al., 2011), Taiwan, --- 30 cases, so PS4 is met PP1_strong - variant segregates with the FH phenotype in 39 informative meiosis from at least 14 families: - 20 informative meiosis from 7 families from Laboratory of Genetics and Molecular Cardiology, University of São Paulo: 16 relatives with the variant have LDL-C >75th percentile, and 4 relatives without the variant have LDL-C <50th percentile; - 1 informative meiosis from Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière): 1 relative positive for variant had LDL-C >75th percentile; - 8 informative meiosis from 3 families from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation): F1 with 2 relatives positive for variant and having LDL-C >75th percentile, and 2 relatives negative for variant and having LDL-C <50th percentile, F2: 1 relative who was positive for the variant and had LDL-C >75th percentile, F3: 2 relatives who were positive for variant with LDL-C >75th percentile, and 1 relative who was negative for the variant with LDL-C <50th percentile; - 2 informative meiosis from 2 families from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge: 1 relative positive for variant with LDL-C >75th percentile in each family; - 8 informative meiosis (unknown how many families) from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA): 5 relatives positive for variant with LDL-C >75th percentile, and 3 relatives were negative for variant with LDL-C <50th percentile. --- 39 segregations, so PP1_Strong is met PM2 - PopMax MAF = 0.00006533 (0.007%) in South Asian exomes (gnomAD v2.1.1). It is below than 0.02%, so PM2 is met. PM3 - variant meets PM2 and was identified in: - 1 index case homozygous for the variant with TC = 700mg/dl at 7 years old from Ambry Genetics. ---> individual is homozygous for variant and has an homozygous phenotype, so PM3 is met. - 2 unrelated index cases, both homozygous for the variant, with LDL-C 352mg/dL under statin treatment (352/0.7 = 503mg/dl) and LDL-C=409mg/dl under statin treatment (409/0.7 = 584mg/dl), respectively, both from Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière) ---> individuals are homozygous for variant and have an homozygous phenotype, so PM3 is me -
not provided Pathogenic:3
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Not observed at significant frequency in large population cohorts (gnomAD); Reported as pathogenic by the ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel (Clinvar Variation ID# 226363); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(A519T); This variant is associated with the following publications: (PMID: 32759540, 34407635, 33807407, 35339733, 33994402, 34456049, 35913489, 27777316, 33303402, 35052492, 25257073, 12124988, 27680772, 29874871, 19007590, 17539906, 27578104, 25461735, 15241806, 18718593, 34426522, Shivraj2011[Review], 32041611, 33740630, 10487776, 37589137, 37409534, 37937776, 37443404, 36254377, 32977124, 32706999, 34040191, 35379577, 9409298, 28958694, 28502495, 34037665, 24075752, 22883975, 33794673, 21376320, 15200491, 15199436, 27765764, 27784735, 16627557, 17094996, 31491741, 27206942, 19318025, 23375686, 23538283, 9544745, Junit2003[CaseReport], 27578128, 11196104, 32331935) -
The LDLR c.1618G>A (p.Ala540Thr) variant (also known as A519T) has been reported in multiple individuals with familial hypercholesterolemia (FH) (PMIDs: 32331935 (2020), 23375686 (2013), 18718593 (2009), 19007590 (2008), 15241806 (2004), 15200491 (2004), 15199436 (2004), 11196104 (2000)). It has also been reported in cases of homozygous and compound heterozygous FH (PMIDs: 32977124 (2020), 24561735 (2015)). A functional study indicated the variant caused reduced LDLR activity (PMID: 9409298 (1997)). 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. The frequency of this variant in the general population, 0.000008 (2/251472 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. Based on the available information, this variant is classified as pathogenic. -
Familial hypercholesterolemia Pathogenic:2
This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 540 of the LDLR protein (p.Ala540Thr). This variant is present in population databases (rs769370816, gnomAD 0.006%). This missense change has been observed in individuals with familial hypercholesterolemia and hyperlipidemia (PMID: 9544745, 11196104, 15200491, 15241806, 18718593, 19007590, 21376320, 23375686, 24075752, 25461735). It has also been observed to segregate with disease in related individuals. This variant is also known as A519T. ClinVar contains an entry for this variant (Variation ID: 226363). 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%. For these reasons, this variant has been classified as Pathogenic. -
Variant summary: LDLR c.1618G>A (p.Ala540Thr) results in a non-conservative amino acid change in 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 8e-06 in 251472 control chromosomes. c.1618G>A has been reported in the literature in multiple individuals affected with Hypercholesterolemia (example, Sun_1998, Merino-Ibarra_2007, Bertolini_2013, Martin_2016). These data indicate that the variant is very likely to be associated with disease. Twelve 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. -
Homozygous familial hypercholesterolemia Pathogenic:1
The p.Ala540Thr variant in LDLR (also described as p.Ala519Thr in the literature) has been reported in >17 individuals with familial hypercholesterolemia (FH) or hyperlipidemia, including in one homozygote and in 1 compound heterozygote with another pathogenic variant and segregated with disease in at least 9 affected relatives from 4 families (Sun 1997 PMID: 9409298, Weiss 2000 PMID: 11196104, Mozas 2004 PMID: 15241806, Dedoussis 2004 PMID: 15200491, Leren 2004 PMID: 15199436, Civeira 2008 PMID: 19007590, Miyake 2009 PMID: 18718593, Chiou 2011 PMID: 21376320, Faiz 2013 PMID: 24075752, Bertolini 2013 PMID: 23375686, Jannes 2015 PMID: 25461735, Martin 2016 PMID: 27680772, Kellogg 2018 (https://doi.org/10.1101/425975)). It has also been reported by other clinical laboratories in ClinVar (Variation ID:226363) and has been identified in 0.007% (2/30616) of South Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). This frequency is low enough to be consistent with the frequency of FH in the general population. In vitro functional studies support an impact on protein function (Sun 1997 PMID: 9409298) and computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant FH. ACMG/AMP Criteria applied: PS4, PP1_Strong, PS3_Supporting, PM2_Supporting. -
Cardiovascular phenotype Pathogenic:1
The c.1618G>A (p.A540T) alteration is located in coding exon 11 of the LDLR gene. This alteration results from a G to A substitution at nucleotide position 1618, causing the alanine (A) at amino acid position 540 to be replaced by a threonine (T). Based on data from gnomAD, the A allele has an overall frequency of 0.001% (2/251472) total alleles studied. The highest observed frequency was 0.007% (2/30616) of South Asian alleles. This alteration, also known as p.A519T, has been detected in a number of individuals with familial hypercholesterolemia (FH) from various ethnic groups (Weiss, 2000; Leren, 2004; Dedoussis, 2004; Civeira, 2008; Wang, 2016; Hori, 2019; Sturm, 2021). Several homozygous FH cases have been reported, including individuals homozygous for p.A540T, as well as compound heterozygotes with other LDLR alterations (Bertolini, 2013; Rocha, 2013; Santos, 2014; Jannes, 2015; Sánchez-Hernández, 2016). This amino acid position is highly conserved in available vertebrate species. Based on internal structural analysis, p.A540T is moderately destabilizing to the local structure (Ambry internal data). In one study, cultured cells from a patient heterozygous for this alteration exhibited reduced LDLR activity and protein expression compared with cells from a control individual (Sun, 1997). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at