19-11105436-C-T
Variant summary
Our verdict is Pathogenic. The variant received 16 ACMG points: 20P and 4B. PS3PS4PP1_StrongPM1PM3BS4PM2PP3PP4
This summary comes from the ClinGen Evidence Repository: NM_000527.5(LDLR): c.530C>T (p.Ser177Leu) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PS3, PS4, PM1, PM2, PM3, PP1_Strong, PP3, PP4 and 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:PS3 - PMID:31578082 - Level 1 assay - Heterologous cells (CHO), FACS assays and CLSM: 65% cell surface LDLR, 10% binding and <2% uptake. PMID:2760205 - Level 2 assay - Homozygous patient fibroblast, 125I-LDL assays: <2% LDLR activity. PMID:25647241 - Level 3 assay - Heterologous cells (HeLa), CLSM assays: LDLR activity decreased compared to WT - considered as disruptive.PS4 - Variant meets PM2. Variant identified in 30 unrelated index cases (5 cases (2 with DLCN≥6; 3 with Simon-Broome possible) 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 case with Simon-Broome possible from GeneDx Inc.; 11 cases with Simon-Broome possible from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge; 13 cases with Simon-Broome possible/definite from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation).PM1 - Variant meets PM2 and is missense in exon 4.PM2 - PopMax MAF = 0.00006533 (0.006533%) in South Asian exomes+genomes (gnomAD v2.1.1).PM3 - Patient 3 from PMID:18263977 has LDL = 19.7 mmol/l and also LDLR p.Arg350* in trans - Pathogenic by these guidelines. Two true homozygotes (FHF23 and FHF57) published in PMID:27816806 had LDL = 16.2 mmol/l and 22.6 mmol/l, respectively.PP1_Strong - Variant segregates with FH phenotype in 52 informative meiosis in 26 families from different labs (Laboratory of Genetics and Molecular Cardiology, University of São Paulo; Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière); Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge): 43 relatives tested positive had LDL-C >75th percentile + 9 relatives tested negative had LDL-C <50th percentile.PP3 - REVEL = 0.886.PP4 - Variant meets PM2. Variant identified in 30 unrelated index cases who fulfill clinical criteria for FH from several labs (see PS4 for details).BS4 - Variant does not segregate with phenotype in 14 informative meiosis from at least 6 families from different labs (Laboratory of Genetics and Molecular Cardiology, University of São Paulo; Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge): 13 relatives tested negative but had LDL-C >75th percentile + 1 relative tested positive but LDL-C <50th percentile.Variant has 3 Strong, 3 Moderate and 2 Supporting evidence codes towards Pathogenic, enough to classify as Pathogenic, and only 1 Strong evidence codes 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/CA023715/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 16 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| LDLR | NM_000527.5 | c.530C>T | p.Ser177Leu | missense_variant | Exon 4 of 18 | ENST00000558518.6 | NP_000518.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| LDLR | ENST00000558518.6 | c.530C>T | p.Ser177Leu | missense_variant | Exon 4 of 18 | 1 | NM_000527.5 | ENSP00000454071.1 |
Frequencies
GnomAD3 genomes 0.0000394 AC: 6AN: 152202Hom.: 1 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000159 AC: 4AN: 251308 AF XY: 0.0000294 show subpopulations
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461728Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7AN XY: 727172 show subpopulations
Age Distribution
GnomAD4 genome 0.0000394 AC: 6AN: 152202Hom.: 1 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74344 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
Age Distribution
ClinVar
Submissions by phenotype
Hypercholesterolemia, familial, 1 Pathogenic:17
subjects mutated among 2600 FH index cases screened = 2 , family members = 3 with co-segregationFH-Puerto-Rico, 2% LDLR Activity / Software predictions: Damaging -
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NM_000527.5(LDLR): c.530C>T (p.Ser177Leu) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes (PS3, PS4, PM1, PM2, PM3, PP1_Strong, PP3, PP4 and 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: PS3 - PMID: 31578082 - Level 1 assay - Heterologous cells (CHO), FACS assays and CLSM: 65% cell surface LDLR, 10% binding and <2% uptake. PMID: 2760205 - Level 2 assay - Homozygous patient fibroblast, 125I-LDL assays: <2% LDLR activity. PMID: 25647241 - Level 3 assay - Heterologous cells (HeLa), CLSM assays: LDLR activity decreased compared to WT - considered as disruptive. PS4 - Variant meets PM2. Variant identified in 30 unrelated index cases (5 cases (2 with DLCN≥6; 3 with Simon-Broome possible) 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 case with Simon-Broome possible from GeneDx Inc.; 11 cases with Simon-Broome possible from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge; 13 cases with Simon-Broome possible/definite from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation). PM1 - Variant meets PM2 and is missense in exon 4. PM2 - PopMax MAF = 0.00006533 (0.006533%) in South Asian exomes+genomes (gnomAD v2.1.1). PM3 - Patient 3 from PMID: 18263977 has LDL = 19.7 mmol/l and also LDLR p.Arg350* in trans - Pathogenic by these guidelines. Two true homozygotes (FHF23 and FHF57) published in PMID: 27816806 had LDL = 16.2 mmol/l and 22.6 mmol/l, respectively. PP1_Strong - Variant segregates with FH phenotype in 52 informative meiosis in 26 families from different labs (Laboratory of Genetics and Molecular Cardiology, University of São Paulo; Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies (APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière); Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge): 43 relatives tested positive had LDL-C >75th percentile + 9 relatives tested negative had LDL-C <50th percentile. PP3 - REVEL = 0.886. PP4 - Variant meets PM2. Variant identified in 30 unrelated index cases who fulfill clinical criteria for FH from several labs (see PS4 for details). BS4 - Variant does not segregate with phenotype in 14 informative meiosis from at least 6 families from different labs (Laboratory of Genetics and Molecular Cardiology, University of São Paulo; Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge): 13 relatives tested negative but had LDL-C >75th percentile + 1 relative tested positive but LDL-C <50th percentile. Variant has 3 Strong, 3 Moderate and 2 Supporting evidence codes towards Pathogenic, enough to classify as Pathogenic, and only 1 Strong evidence codes towards Benign. The Pathogenic criteria overwhelms the Benign criteria, so we are confident in classifying this variant as Pathogenic. -
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0/190 non-FH alleles, 0/32 normolipidemic individuals; 0/60 healthy control individuals -
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The c.530C>T (p.Ser177Leu) variant, also known as p.Ser156Leu in the LDLR gene, that encodes for low density lipoprotein receptor, has been identified in heterozygous, compound heterozygous or homozygous state in numerous individuals (>30) who fulfill the clinical criteria of familial hypercholesterolemia (FH) and segregated with disease in multiple families (PMID: 8096412, 15241806, 17765246, 18263977, 22698793, 25461735, 25487149, 25647241, 2760205, 31578082, 27816806, 28235710, 9654205, 20145306). This variant has been reported in compound heterozygosity with a truncating variant (p.Arg350*) which is classified as pathogenic by the ClinGen Variant Curation Expert Panel (ClinVar ID:226342), in an individual with severe FH (LDL-C: 19.7mmol/l) (PMID: 18263977). Experimental studies using transfected LDLR-deficient CHO cells (CHO-ldlA7), true homozygous patient fibroblasts and transfected HeLa-Kyoto cells revealed that this variant causes significantly reduced LDLR expression, LDL binding and internalization (PMID: 31578082, 2760205, 25647241). This variant lies in the well-established LDL binding domain (amino acids 105-232) critical for protein function (PMID: 2600087). In-silico computational prediction tools suggest that the p.Ser177Leu variant may have deleterious effect on the protein function (REVEL score: 0.886). This variant is found to be rare (4/251308; 0.001592%) in the gnomAD database. This variant is reported in ClinVar as pathogenic (ID: 3686) by multiple submitters (23) and reviewed by the expert panel. Therefore, the c.530C>T (p.Ser177Leu) variant in the LDLR gene is classified as pathogenic. -
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The p.Ser177Leu variant in LDLR (also described as p.Ser156Leu in the literature) has been reported in several individuals with familial hypercholesterolemia (FH): In at least 15 in the heterozygous state (Schuster 1993 PMID: 8096412, Kuhrova 2002 PMID: 11754108, Bourbon 2008 PMID: 17765246, Tichy 2012 PMID: 22698793, Jannes 2015 PMID: 25461735, Thormaehlen 2015 PMID: 25647241, Sharifi 2016 PMID: 26892515), 1 with homozygous FH (Hobbs 1989 PMID: 2760205), and 2 in the compound heterozygous state (Jannes 2015 PMID: 25461735, Kubalska 2008 PMID: 18263977) and has also been reported by other clinical laboratories in ClinVar (Variation ID 3686). This variant segregated with disease in at least 9 affected relatives from 2 families (Hobbs 1992 PMID: 1301956, Schuster 1993 PMID: 8096412). However, not all family members that carried the variant presented with high cholesterol levels (Hobbs 1989 PMID: 2760205). This variant has also been identified in in 0.02% (3/15272) of Latino/Admixed American chromosomes by gnomAD (http://gnomad.broadinstitute.org, v3.1.2). 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.Ser177Leu variant may impact protein function (Hobbs 1989 PMID: 2760205, Kubalska 2008 PMID: 18263977, Thormaehlen 2015 PMID: 25647241) and computational prediction tools and conservation analysis are consistent with pathogenicity. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant FH. The ACMG/AMP Criteria applied: PS4, PP1_strong, PS3_supporting, PP3, PM2_Supporting. -
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This missense change has been observed in individuals with familial hypercholesterolemia -
Familial hypercholesterolemia Pathogenic:6
This c.530C>T (p.Ser177Leu) variant in exon 4 of the LDLR gene results in an amino acid change at residue 177 of a serine to a leucine. This variant has been reported in multiple patients and families with familial hypercholesterolemia (PMID: 8096412, 9654205, 15199436, 15241806, 17765246, 22698793, 25487149) and is rarely observed in general population databases. Functional assays have also shown that this variant is disruptive (PMID: 25647241). Therefore, the c.530C>T (p.Ser177Leu) variant in the LDLR gene is classified as pathogenic. -
The LDLR c.530C>T p.(Ser177Leu) variant has been reported in >=10 FH patients meeting clinical criteria, including patients where secondary causes of high cholesterol were excluded (PS4_STRONG, PP4_SUPPORTING; PMIDs 1319734, 9654205, 15241806, 22698793, 27824480, 33533259, 30975109, ClinGen FH VCEP data, internal data). This variant was found to segregate with FH in >=6 informative meioses in >=1 family (PP1_STRONG; PMID 2760205, 8096412, 18263977, 30975109, ClinGen FH VCEP data) and was observed in the homozygous and compound heterozygous state in individuals with a homozygous FH phenotype including where parental testing confirmed variants were in trans (PM3_MODERATE; PMIDs 2760205, 18263977, 19026292, 27816806, 31578082, 36901902). Lack of segregation in >=2 families, with 2>= informative meioses in each family (BS4_STRONG; PMID 2760205, ClinGen FH VCEP data). Level 1 functional study in CHO-ldlA7 cells demonstrated reduced LDLR expression, LDL-binding and LDLR uptake, <70% of wild-type (PS3_STRONG; PMID 31578082). This missense variant is located in exon 4 (PM1_MODERATE) and has a REVEL score of 0.886 (PP3_SUPPORTING). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00006533 in the South Asian population, which is lower than the ClinGen FH VCEP threshold (=<0.0002) for PM2_MODERATE. Although there are both pathogenic and benign types of evidence for this variant, there is sufficient evidence overall to support a classification of Pathogenic. -
This missense variant replaces serine with leucine at codon 177 of the LDLR protein. This variant is also known as p.Ser156Leu in the mature protein, and as FH Puerto Rico in the literature. This variant alters a conserved serine residue in the LDLR type A repeat 4 of the LDLR protein (a.a. 146-186), where pathogenic missense variants are found enriched (ClinVar-LDLR). Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. Experimental functional studies have shown that this variant causes a significant reduction in LDLR expression, binding, and uptake (PMID: 2760205, 25647241, 31578082). This LDLR variant has been reported in over 40 heterozygous individuals affected with familial hypercholesterolemia (PMID: 2760205, 15241806, 17765246, 22698793, 25647241, 2760205, 28235710, 30975109, 31578082, 34037665, 35741760, 36901902, 37568561, 37967952; Color internal data). This variant has also been observed in compound heterozygous state with a known pathogenic LDLR variant as well as in homozygosity in multiple individuals affected with severe homozygous familial hypercholesterolemia, a phenotype expected of having two deleterious LDLR variants (PMID: 18263977, 25461735, 2760205, 27816806, 36901902). It has been shown that this variant segregates with disease in over 17 affected individuals across 3 large families (PMID: 2760205, 30975109, 36901902). This variant has been identified in 4/251308 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -
This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 177 of the LDLR protein (p.Ser177Leu). This variant is present in population databases (rs121908026, gnomAD 0.006%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 2760205, 15241806, 17765246, 22698793, 25487149, 25647241). 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. ClinVar contains an entry for this variant (Variation ID: 3686). 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: 2760205, 25647241). For these reasons, this variant has been classified as Pathogenic. -
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Variant summary: The LDLR c.530C>T (p.Ser177Leu) variant involves the alteration of a conserved nucleotide. Ser177 is a highly conserved amino acid across species, and 4/4 in silico tools predict a damaging outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 1/121078 control chromosomes at a frequency of 0.0000083, which does not exceed the estimated maximal expected allele frequency of a pathogenic LDLR variant (0.0012508). This variant has been reported in numerous patients heterozygously or homozygously. Functional studies showed this variant with defective maturation and LDL metabolism. Taken together, this variant is classified as pathogenic. -
not provided Pathogenic:3Other:1
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PS3_moderate, PS4_moderate, PM1, PM2, PM3, PP1, PP3 -
The frequency of this variant in the general population, 0.000065 (2/30616 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in in individuals/families with familial hypercholesterolemia (PMIDs: 30592178 (2019), 22698793 (2012), 20145306 (2010), 17765246 (2008), 15241806 (2004), 9654205 (1998), 8096412 (1993), and 2760205 (1989)) as well as individuals who were homozygous or compound heterozygous with a second pathogenic LDLR variant (PMIDs: 27816806 (2016), 18263977 (2008), 9654205 (1998), and 2760205 (1989)). In addition, experimental studies have determined this variant results in reduced LDL binding (PMIDs: 25647241 (2015) and 1301956 (1992)). Based on the available information, this variant is classified as pathogenic. -
Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies demonstrate defective receptor transport and ligand binding (Hobbs et al., 1989; Hobbs et al., 1992; Li et al., 2004; Thormaehlen et al., 2015); Disrupts a negatively charged triplet, Ser-Asp-Glu, located at the carboxyl-terminal end of the LDL-receptor class A4 repeat domain that is critical for ligand binding (Schneider et al., 2003); This variant is associated with the following publications: (PMID: 25647241, 15199436, 25487149, 30592178, 31491741, 30512145, 30975109, 8096412, 8828982, 14512370, 2760205, 1301956, 9654205, 14508510, 7947594, 14993243, 15241806, 15556092, 15556093, 16627557, 17335829, 17539906, 17765246, 18263977, 18279815, 19026292, 20145306, 21310417, 22698793, 25461735, 26892515, 27816806, 31447099, 32041611, 32660911, 32331935, 33740630, 34037665) -
Cardiovascular phenotype Pathogenic:1
The p.S177L pathogenic mutation (also known as c.530C>T), located in coding exon 4 of the LDLR gene, results from a C to T substitution at nucleotide position 530. The serine at codon 177 is replaced by leucine, an amino acid with dissimilar properties. This alteration impacts a residue in the conserved cluster of acidic amino acids at the C-terminal end of LDLR class A repeat 4 (Jeon H and Blacklow C. Annu. Rev. Biochem. 2005;74:535-62). This variant (also described as legacy p.S156L and FH Puerto Rico) has been reported in multiple individuals with familial hypercholesterolemia of different origins, some of whom were homozygous for this alteration (Hobbs HH et al. J. Clin. Invest., 1989 Aug;84:656-64; Schuster H et al. Clin Investig, 1993 Feb;71:172-5; Górski B et al. Hum. Genet., 1998 May;102:562-5; Chmara M et al. J. Appl. Genet., 2010;51:95-106; Setia N et al. Atherosclerosis, 2016 Dec;255:31-36; Banerjee P et al. Arterioscler Thromb Vasc Biol, 2019 11;39:2248-2260). In at least two families, this alteration was described to segregate with the disease across multiple generations (Hobbs HH et al. J. Clin. Invest., 1989 Aug;84:656-64; Mohd Nor NS et al. BMC Pediatr, 2019 04;19:106). In addition, functional studies have revealed deficient protein maturation and ligand binding by this alteration (Hobbs HH et al. J. Clin. Invest., 1989 Aug;84:656-64; Thormaehlen AS et al. PLoS Genet., 2015 Feb;11:e1004855; Banerjee P et al. Arterioscler Thromb Vasc Biol, 2019 11;39:2248-2260). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at