19-11110738-G-A
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 20P and 4B. PS3PS4PP1_StrongBS4PM2PM5PM3PP3PP4
This summary comes from the ClinGen Evidence Repository: The NM_000527.5 (LDLR):c.1027G>A (p.Gly343Ser) variant is classified as Pathogenic (modified) for Familial Hypercholesterolemia by applying evidence codes (PM2, PP3, PS3, PP4, PS4, PP1_Strong, PM5, PM3, BS4) 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:PM2: PopMaxMAF=0.00005 in East Asian population from gnomAD (gnomAD v2.1.1).PP3: REVEL=0.929, it is above 0.75.PS3: Level 1 assays: PMID 15100232. Heterologous cells (CHO) were used in WB, FACS and NMR Spectroscopy. The experiments shown <60% cell surface LDLR expression (Fig 5C), and >80% expressed receptor bind and release LDL upon low pH condition (Fig 6B), the amount of LDL bound to the mutant receptor correlates tightly with cell-surface LDLR expression, NMR indicates misfolding defects of the receptor. Functional data is consistent with damaging effect. This study is reported by Boswell et al, 2004, from Department of Biochemistry, Division of Structural Biology, University of Oxford, UK. PP4: Variant meets PM2 and is identified in at least ˃1 index cases who fulfil criteria for FH after alternative causes of high cholesterol were excluded.PS4: Variant meets PM2 and is identified in at least 26 index cases reported in VCI and PubMed. There are 14 unrelated index case reported in VCI who fulfil criteria for FH diagnosis: Twelve cases fulfil DLCN criteria, 7 reported from Service de Biochimie et de Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France, 1 from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA), 2 from Research Lab of Molecular Genetics of Lipid Metabolism; and 2 from Robarts Research Institute, Canada; two cases fulfil Simon Broome possible criteria, reported from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge. Variant is reported in PubMed in at least 12 index cases fulfil criteria for FH diagnosis: 8 cases fulfil DLCN probable/definite FH criteria in PMID 11040093, 11810272, 32977124, 30270055, 27784735; 1 case fulfil Simon Broome possible FH criteria in PMID 26748104; 3 cases fulfil MedPed criteria in PMID 8882879, 27824480. PP1_Strong: Variant segregates with FH phenotype in 18 informative meiosis from 6 families reported from 4 different labs in VCI: 11 affected carries and 7 unaffected non-carriers reported from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA), Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge, Laboratory of Genetics and Molecular Cardiology, and Research Lab of Molecular Genetics of Lipid Metabolism. PM5: Three other variants at the same codon: NM_000527.5(LDLR):c.1028G>T (p.Gly343Val)(ClinVarID 440618) classified as Likely Pathogenic, NM_000527.5(LDLR):c.1028G>A (p.Gly343Asp)(ClinVarID 251606) is classified as Likely Pathogenic, NM_000527.5(LDLR):c.1027G>T (p.Gly343Cys)(ClinVarID 251605) is classified as Pathogenic, by these guidelines, therefore PM5 is met.PM3: Variant meets PM2 and is identified in an index case with homozygous FH phenotype (untreated LDL-C > 500mg/dL, or LDL-C > 300 mmol/dL on high-intensive lipid-lowering therapy and the presence of tendon xanthomas before 10 year of age), reported by Sanchez-Hernandez et al, 2016, Universitario Insular Materno Infantil de Gran Canaria, Spain, PMID 27784735. This variant met enough pathogenic criteria toward Pathogenic classification by these guidelines before PM3 code applied.BS4: Variant does not segregate with FH phenotype in total of 6 informative meiosis reported in VCI. Five affected relatives without the variant and had LDL-C>75th percentile, 2 cases from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA), 1 case each from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge, Laboratory of Genetics and Molecular Cardiology, and Research Lab of Molecular Genetics of Lipid Metabolism. There is 1 instance reported from 1 laboratory, where an unaffected family member had LDL-C<50th percentile and carries the variant, reported in VCI from Laboratory of Genetics and Molecular Cardiology, GTR LabID 505581.Variant has 3 Strong, 3 Moderate and 2 Supporting evidence codes toward Pathogenic, enough to classify as Pathogenic, and only 1 Strong evidence code towards Benign. The Pathogenic criteria overwhelms the Benign criteria, so we are confident in classifying this variant as Pathogenic. LINK:https://erepo.genome.network/evrepo/ui/classification/CA023406/MONDO:0007750/013
Frequency
Consequence
NM_000527.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LDLR | NM_000527.5 | c.1027G>A | p.Gly343Ser | missense_variant | Exon 7 of 18 | ENST00000558518.6 | NP_000518.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.0000197 AC: 3AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251066Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135780
GnomAD4 exome AF: 0.0000356 AC: 52AN: 1461494Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 727050
GnomAD4 genome 0.0000197 AC: 3AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
Hypercholesterolemia, familial, 1 Pathogenic:17Uncertain:4
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The NM_000527.5 (LDLR):c.1027G>A (p.Gly343Ser) variant is classified as Pathogenic (modified) for Familial Hypercholesterolemia by applying evidence codes (PM2, PP3, PS3, PP4, PS4, PP1_Strong, PM5, PM3, BS4) 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: PM2: PopMaxMAF=0.00005 in East Asian population from gnomAD (gnomAD v2.1.1). PP3: REVEL=0.929, it is above 0.75. PS3: Level 1 assays: PMID 15100232. Heterologous cells (CHO) were used in WB, FACS and NMR Spectroscopy. The experiments shown <60% cell surface LDLR expression (Fig 5C), and >80% expressed receptor bind and release LDL upon low pH condition (Fig 6B), the amount of LDL bound to the mutant receptor correlates tightly with cell-surface LDLR expression, NMR indicates misfolding defects of the receptor. Functional data is consistent with damaging effect. This study is reported by Boswell et al, 2004, from Department of Biochemistry, Division of Structural Biology, University of Oxford, UK. PP4: Variant meets PM2 and is identified in at least >1 index cases who fulfil criteria for FH after alternative causes of high cholesterol were excluded. PS4: Variant meets PM2 and is identified in at least 26 index cases reported in VCI and PubMed. There are 14 unrelated index case reported in VCI who fulfil criteria for FH diagnosis: Twelve cases fulfil DLCN criteria, 7 reported from Service de Biochimie et de Biologie Moléculaire, Hospices Civils de Lyon, Lyon, France, 1 from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA), 2 from Research Lab of Molecular Genetics of Lipid Metabolism; and 2 from Robarts Research Institute, Canada; two cases fulfil Simon Broome possible criteria, reported from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge. Variant is reported in PubMed in at least 12 index cases fulfil criteria for FH diagnosis: 8 cases fulfil DLCN probable/definite FH criteria in PMID 11040093, 11810272, 32977124, 30270055, 27784735; 1 case fulfil Simon Broome possible FH criteria in PMID 26748104; 3 cases fulfil MedPed criteria in PMID 8882879, 27824480. PP1_Strong: Variant segregates with FH phenotype in 18 informative meiosis from 6 families reported from 4 different labs in VCI: 11 affected carries and 7 unaffected non-carriers reported from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA), Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge, Laboratory of Genetics and Molecular Cardiology, and Research Lab of Molecular Genetics of Lipid Metabolism. PM5: Three other variants at the same codon: NM_000527.5(LDLR):c.1028G>T (p.Gly343Val)(ClinVarID 440618) classified as Likely Pathogenic, NM_000527.5(LDLR):c.1028G>A (p.Gly343Asp)(ClinVarID 251606) is classified as Likely Pathogenic, NM_000527.5(LDLR):c.1027G>T (p.Gly343Cys)(ClinVarID 251605) is classified as Pathogenic, by these guidelines, therefore PM5 is met. PM3: Variant meets PM2 and is identified in an index case with homozygous FH phenotype (untreated LDL-C > 500mg/dL, or LDL-C > 300 mmol/dL on high-intensive lipid-lowering therapy and the presence of tendon xanthomas before 10 year of age), reported by Sanchez-Hernandez et al, 2016, Universitario Insular Materno Infantil de Gran Canaria, Spain, PMID 27784735. This variant met enough pathogenic criteria toward Pathogenic classification by these guidelines before PM3 code applied. BS4: Variant does not segregate with FH phenotype in total of 6 informative meiosis reported in VCI. Five affected relatives without the variant and had LDL-C>75th percentile, 2 cases from Cardiovascular Genetics Laboratory (PathWest Laboratory Medicine WA), 1 case each from Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge, Laboratory of Genetics and Molecular Cardiology, and Research Lab of Molecular Genetics of Lipid M -
This missense variant replaces glycine with serine at codon 343 in the EGF-like repeat A of the LDLR protein. This variant is also known as p.Gly322Ser in the mature protein, and as and as FH-Picardie in the literature. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. A functional study has shown a significantly reduced LDLR activity (15-30% of wild type) in cells from an individual compound heterozygous for this variant and another pathogenic LDLR variant (PMID: 1301956). This variant has been shown to cause LDLR protein mis-folding and partial reduction in cell surface expression of the protein (PMID: 15100232). This variant has been reported in over 20 individuals affected with familial hypercholesterolemia (PMID: 1301956, 11040093, 11933210, 15241806, 17765246, 18096825, 20506408, 22294733, 23375686, 25461735, 27765764, 30270055, 30293936, 32675963; Color internal data). It has been shown that this variant segregates with disease in multiple affected individuals across multiple families (ClinVar SCV004022448.1). This variant has also been observed in both homozygous and compound heterozygous state with a known pathogenic LDLR variant in two individuals affected with severe homozygous familial hypercholesterolemia, a phenotype expected of having two deleterious LDLR variants (PMID: 27784735). Different variants affecting the same codon (p.Gly343Asp, p.Gly343Cys, and p.Gly343Val), have been reported as disease-causing (ClinVar variation ID: 251606, 251605, 440618), suggesting that glycine at this position is important for LDLR function. This variant has been identified in 8/282454 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -
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This variant (LDLR):c.1027G>A (p.Gly343Ser) variant is classified as Pathogenic (modified) for Familial Hypercholesterolemia by applying evidence codes (PM2, PP3, PS3, PP4, PS4, PP1_Strong, PM5, PM3, BS4) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). -
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0/190 non-FH alleles; 0/200 Brazilian (european ancestry) normolipidemic individuals -
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The missense point mutations c.G1027A (p.G343S) was identified in a family with familial hypercholesterolemia. According to the American College of Medical Genetics and Genomics (ACMG) pathogenicity rating criteria and guidelines, it was predicted that the c.G1027A mutation was pathogenic. These mutations affected LDLR binding to LDL containing APOB and APOE, resulting in the disturbance of LDL metastasis in blood and excessive siltation in tissues, leading to multiple cutaneous xanthoma and atherosclerosis. The discovered mutations in LDLR enriched -
subjects mutated among 2600 FH index cases screened = 7 , family members = 12 with co-segregation (1 homozygote in a family) / FH-Picardie, 15 to 30% LDLR activity / Software predictions: Damaging -
PS4+PS3_Moderate+PM5_Strong+PM2_Supporting -
PS3, PS4, PM2, PM3, PP3, PP4, PP1_Strong -
not provided Pathogenic:8Other:1
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Published functional studies demonstrate that this variant affects protein folding and cell surface expression, resulting in decreased LDL receptor activity (Hobbs et al., 1992; Boswell et al., 2004); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 11040093, 29353225, 11851376, 15241806, 18757057, 22294733, 19446849, 29874871, 30270055, 22390909, 15100232, 17765246, 27741487, 21382890, 23375686, 25487149, 26748104, 8882879, 11933210, 20506408, 25461735, 16627557, 27824480, 18096825, 11810272, 15890894, 23833242, 24627126, 25647241, 30586733, 27765764, 27784735, 31447099, 32977124, 32041611, 33303402, 32719484, 32522009, 32770674, 1301956, 33740630, 34037665, 27535533) -
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LDLR: PM2, PM5, PP1:Moderate, PS4:Moderate, PP4, PS3:Supporting -
The LDLR c.1027G>A (p.Gly343Ser) variant has been reported in the published literature in multiple individuals and families with hypercholesterolemia (PMIDs: 36105085 (2022), 30710474 (2019), 30270055 (2018), 29353225 (2018), 27824480 (2017), 27784735 (2016), 27765764 (2016), 25461735 (2015), 20506408 (2010), 15241806 (2004), 11040093 (2000)). Experimental studies indicate the variant is damaging to LDLR function (PMIDs: 15100232 (2004), 1301956 (1992)). The frequency of this variant in the general population, 0.000047 (6/128994 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on LDLR mRNA splicing yielded predictions that this variant may result in the gain of a cryptic splice site without affecting the natural splice sites. Based on the available information, this variant is classified as pathogenic. -
Familial hypercholesterolemia Pathogenic:4Uncertain:1
This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 343 of the LDLR protein (p.Gly343Ser). This variant is present in population databases (rs730882096, gnomAD 0.005%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 1301956, 11040093, 11933210, 15241806, 17765246, 18096825, 20506408, 22294733, 23375686, 25461735, 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 G322S or FH-Picardie. ClinVar contains an entry for this variant (Variation ID: 183106). 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%. Experimental studies have shown that this missense change affects LDLR function (PMID: 15100232). This variant disrupts the p.Gly343 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been observed in individuals with LDLR-related conditions (PMID: 12436241, 18718593), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. -
Variant summary: The LDLR c.1027G>A (p.Gly343Ser) variant involves the alteration of a conserved nucleotide, resulting in a missense substitution that lies within the EGF-like calcium-binding domain, the EGF-like domain, and the Growth factor receptor cysteine-rich domain (InterPro). 5/5 in silico tools predict a damaging outcome for this variant. This variant was found in the large control database ExAC at a frequency of 0.0000246 (3/121826 control chromosomes), which does not exceed the estimated maximal expected allele frequency of a pathogenic LDLR variant (0.0012508). The variant is present in patient cohorts affected with familial hypercholesterolemia (e.g., Bertolini_Arthero_2013; Salazar_HM_2002; Huijgen_HM_2010 amongst others) and is widely considered to be a pathogenic mutation in the literature. A functional study showed that the variant causes a ~50% reduction in LDL receptor protein at the cell surface likely due to protein misfolding, though the receptor that is present at the cell surface is able to bind and release LDL cholesterol properly (Boswell_JBC_2004). In addition, 2 other missense mutations at the Gly343 residue have been identified in patients with familial hypercholesterolemia (p.Gly343Cys [Jelassi_Artherosclerosis_2008] and p.Gly343Asp [Amsellem_HG_2002]), suggesting the residue is a critical amino acid in the development of hypercholesterolemia. Multiple clinical diagnostic laboratories/reputable databases have classified this variant with conflicting interpretations in ClinVar, including uncertain significance, likely pathogenic, and pathogenic. Taken together, this variant is classified as pathogenic. -
This missense variant (also known as p.Gly322Ser in the mature protein and as FH-Picardie) replaces glycine with serine at codon 343 of the LDLR protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). A functional study has shown a significantly reduced LDLR activity (15-30% of wild type) in cells from an individual compound heterozygous for this variant and another pathogenic LDLR variant p.Asp304Glu (PMID: 1301956). This variant has been shown to cause LDLR protein mis-folding and partial reduction in cell surface expression of the protein (PMID: 15100232). The mutant receptor present at the cell surface was functional with regard to its ability to bind and release LDL. This variant has been reported in over 20 individuals affected with familial hypercholesterolemia (PMID: 1301956, 11040093, 11933210, 15241806, 17765246, 18096825, 20506408, 22294733, 23375686, 25461735, 27765764, 31893465, 32770674, 34037665, 34297352). Different variants affecting the same codon (p.Gly343Asp, p.Gly343Cys, and p.Gly343Val), have been reported as disease-causing (ClinVar variation ID: 251606, 251605, 440618), suggesting that glycine at this position is important for LDLR function. This variant has been identified in 8/282454 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -
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Homozygous familial hypercholesterolemia Pathogenic:1
The p.Gly343Ser variant in LDLR (also described as p.Gly332Ser in the literature) has been reported across multiple ethnic groups in numerous individuals with familial hypercholesterolemia (FH). Most reports in patient cohorts were in the heterozygous state, with 2 compound heterozygous and 1 homozygous reports respectively (Hobbs 1992, Reshef 1996, Thiart 2000, Van Gaal 2001, Fouchier 2001, Salazar 2002, Mozas 2004, Junyent 2008, Bourbon 2008, Guardamagna 2009, Huijgen 2010, Hollants 2012, Bertolini 2013, Jannes 2015, Wang 2016, Sánchez-Hernández 2016, GabÄová 2017, ClinVar: submission accessions SCV000503283.1, SCV000583777.1 and SCV000268593.1). This variant segregated with disease in at least 4 affected family members from 3 families (Bourbon 2008, Bertolini 2013, GabÄová 2017). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 183106) and has been identified in 0.004% (5/126580) 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. In vitro functional studies provide some evidence that the p.Gly343Ser variant affects protein folding and expression at the cell surface and results in decreased LDL receptor activity (Hobbs 1992; Boswell 2004). Computational prediction tools and conservation analysis suggest that the p.Gly343Ser variant may impact the protein. In addition, 3 other missense variants at this codon (p.Gly343Asp, p.Gly343Val, pGly343Cys) have been identified in patients with FH (Stenson 2017), suggesting that changes at this position are not tolerated. In summary, the p.Gly343Ser variant meets criteria to be classified as pathogenic for autosomal dominant FH based upon presence in multiple affected individuals, segregation studies, low frequency in controls, and functional and computational evidence. ACMG/AMP Criteria applied: PS4, PM2, PP3, PS3_supporting, PP1_Moderate. -
LDLR-related disorder Pathogenic:1
The LDLR c.1027G>A variant is predicted to result in the amino acid substitution p.Gly343Ser. This variant has been repeatedly reported in many individuals with hypercholesterolemia (Variant is also reported as G322S, Hobbs et al. 1992. PubMed ID: 1301956; Huijgen et al. 2012. PubMed ID: 22390909; Salazar et al. 2002. PubMed ID: 11933210; Supplementary Table 1, Kusters et al. 2013. PubMed ID: 23833242; Sánchez-Hernández et al. 2016. PubMed ID: 27784735) and has been interpreted as pathogenic by the ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/183106/). Functional studies indicate this variant disrupts protein function (Reported as G322S in Boswell et al. 2004. PubMed ID: 15100232). This variant is reported in 0.0050% of alleles in individuals of East Asian descent in gnomAD. This variant is interpreted as pathogenic. -
Cardiovascular phenotype Pathogenic:1
The c.1027G>A (p.G343S) alteration is located in exon 7 (coding exon 7) of the LDLR gene. This alteration results from a G to A substitution at nucleotide position 1027, causing the glycine (G) at amino acid position 343 to be replaced by a serine (S). Based on data from gnomAD, the A allele has an overall frequency of 0.003% (8/282454) total alleles studied. This alteration has been reported in a number of individuals with familial hypercholesterolemia (Hobbs, 1992; Reshef, 1996; Thiart, 2000; Fouchier, 2001; Nissen, 1998; Mozas, 2004; Bourbon, 2008; Bertolini, 2013; Huijgen, 2011; Hooper, 2012). Reduced LDLR activity was identified in some of those individuals (Hobbs, 1992; Thiart, 2000). This amino acid position is highly conserved in available vertebrate species. An in vitro study suggested that this alteration would interfere with protein folding and thus surface expression (Boswell, 2004). 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