Submissions for variant NM_000527.5(LDLR):c.268G>A (p.Asp90Asn)

gnomAD frequency: 0.00002  dbSNP: rs749038326

Total submissions: 19

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	RCV000238573	SCV002568016	pathogenic	Hypercholesterolemia, familial, 1	2022-08-28	reviewed by expert panel	curation	The NM_000527.5(LDLR):c.268G>A (p.Asp90Asn) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes PM5_Strong, PM2, PP1_Moderate, PS3_Moderate, PS4_Moderate and PP4 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: PM5_strong - there are 4 other missense variants is the same codon: - NM_000527.5(LDLR):c.268G>T (p.Asp90Tyr) - classified as Likely pathogenic by the FH VCEP, with these guidelines - NM_000527.5(LDLR):c.269A>C (p.Asp90Ala) - Likely pathogenic by these guidelines - NM_000527.5(LDLR):c.269A>G (p.Asp90Gly) - Pathogenic by these guidelines - NM_000527.5(LDLR):c.270T>A (p.Asp90Glu) - Pathogenic by these guidelines --- There are 2 variants classified as Pathogenic, so PM5_Strong is met. PP1_moderate - Variant segregates with phenotype in 4 informative meiosis from different labs: - 1 unaffected family member does not have the variant, from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); - 3 informative meiosis from 1 family from PMID 12837857 (Chang et al. 2003): 1 relative has the variant and phenotype (III:1), plus 2 relatives do not have the variant and do not have the phenotype (II:1 and III:2) 4 informative meiosis, so PP1_Moderate is met. PM2 - PopMax MAF = 0.0008019 (0.08019%) in East Asian (gnomAD v2.1.1), but this is a founder variant in East Asian populations, so PM2 can be met in this instance. PS3_moderate - Level 2 FS: Chang et al., 2003 (PMID:12837857): Heterologous cells (COS-7), FACS assays - results: 55% LDLR cell surface and uptake. Binding is not studied, so not all cycle is studied (level 2 and not level 1) ---- functional study is consistent with damaging effect, activity is below 70% of wild-type, so PS3_Moderate is met. PS4_moderate - variant meets PM2 and was identified in: - 1 index case who fulfills Simon Broome criteria of possible FH from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation), Czech Republic; - 3 unrelated index cases, all with Dutch lipid clinic network >=6, from Robarts Research Institute, Canada; - at least 1 index case with DLCN score of definite FH from U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille (SCV000583645.1 in ClinVar), France; - 1 index case who fulfills SB criteria of at least possible FH from PMID 9259195 (Day et al., 1997), UK; - 1 index case who fulfills SB criteria of at least possible FH from PMID 25962062 (Han et al., 2015), Korea; - 2 unrelated index cases who fulfill SB criteria of possible FH (TC>8mmol/L, plus CAD) from PMID 12837857 (Chang et al., 2003), Taiwan, China; 9 cases, so PS4_Moderate is met. PP4 - variant meets PM2 and was identified in 9 unrelated index cases from different labs (see PS4 for details), so PP4 is met.
LDLR-LOVD, British Heart Foundation	RCV000238573	SCV000294569	likely pathogenic	Hypercholesterolemia, familial, 1	2016-03-25	criteria provided, single submitter	literature only
Robarts Research Institute, Western University	RCV000238573	SCV000484708	likely pathogenic	Hypercholesterolemia, familial, 1		criteria provided, single submitter	clinical testing
Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix	RCV000238573	SCV000503122	likely benign	Hypercholesterolemia, familial, 1	2016-12-16	criteria provided, single submitter	clinical testing	subject mutated among 2600 FH index cases screened = 1 , family members = 2 with co-segregation / other mutations at same codon / Software predictions: Damaging
GeneDx	RCV000494304	SCV000582689	pathogenic	not provided	2023-02-17	criteria provided, single submitter	clinical testing	Described as one of the most frequent variants associated with FH in the Han Chinese population (Chiou and Charng, 2016); Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate reduced receptor protein on cell surface and reduced LDL binding and internalization (Chang et al., 2003); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(Asp69Asn); This variant is associated with the following publications: (PMID: 22390909, 9259195, 24956927, 28235710, 34037665, 12837857, 32977124, 32041611, 33391346, 33994402, 32759540, 23375686, 27206935)
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	RCV000238573	SCV000583645	pathogenic	Hypercholesterolemia, familial, 1	2017-03-30	criteria provided, single submitter	clinical testing
Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	RCV000238573	SCV000599321	likely pathogenic	Hypercholesterolemia, familial, 1	2016-03-01	criteria provided, single submitter	curation
Invitae	RCV000776467	SCV000816377	pathogenic	Familial hypercholesterolemia	2024-01-24	criteria provided, single submitter	clinical testing	This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 90 of the LDLR protein (p.Asp90Asn). This variant is present in population databases (rs749038326, gnomAD 0.08%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 9259195, 9763532, 12436241, 12837857, 15823276, 16343504, 21376320, 22390909, 23375686, 25962062, 27206935, 27765764). This variant is also known as p.Asp69Asn. ClinVar contains an entry for this variant (Variation ID: 251105). 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%. Experimental studies have shown that this missense change affects LDLR function (PMID: 12837857). This variant disrupts the p.Asp90 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 1301956, 8347689, 19026292). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Color Diagnostics, LLC DBA Color Health	RCV000776467	SCV000912016	pathogenic	Familial hypercholesterolemia	2023-09-01	criteria provided, single submitter	clinical testing	This missense variant replaces aspartic acid with asparagine at codon 90 in the second LDLR type A of the ligand binding domain of the LDLR protein. This variant is also known as p.Asp69Asn in the mature protein. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). A functional study has shown that the mutant protein is trapped in the endoplasmic reticulum and shows weak cell surface expression (PMID: 12837857). Cells from an individual compound heterozygous for this variant and p.Cys222* showed no detectable LDLR activity (PMID: 16343504). This variant has been reported in over thirty individuals of varying ethnicities affected with familial hypercholesterolemia (PMID: 9259195, 9763532, 12436241, 12837857, 15823276, 16250003, 16343504, 21376320, 23375686, 25962062, 27206935, 31345425) and is thought to be one of the most common pathogenic mutation in the Chinese population (PMID: 27206935, 30592178, 31686828). This variant has been reported to segregate with disease in one family (PMID: 12837857). This variant has been identified in 17/282878 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different missense variants occurring at this codon, p.Asp90Gly and p.Asp90AGlu, are known to cause disease (ClinVar variation ID: 226313, 251107), suggesting that aspartic acid at this position is important for LDLR protein function. Based on the available evidence, this variant is classified as Pathogenic.
Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	RCV000238573	SCV001432642	pathogenic	Hypercholesterolemia, familial, 1	2019-01-15	criteria provided, single submitter	research
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000776467	SCV001983509	pathogenic	Familial hypercholesterolemia	2021-09-08	criteria provided, single submitter	clinical testing	Variant summary: LDLR c.268G>A (p.Asp90Asn) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.6e-05 in 251486 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in LDLR causing Familial Hypercholesterolemia (5.6e-05 vs 0.0013), allowing no conclusion about variant significance. c.268G>A has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia (Mak_1998, Chiou_2016, Fouchier_2005, Chiou_2010). Functional studies have shown the variant to impact LDLR subcellular localization and reduces LDLR activity (Chang_2003). Other variants have been reported in association with Hypercholesterolemia (D90A, D90E, D90G, D90Y). Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Seven submitters classified as likely pathogenic/pathogenic while one classified as likely benign. Based on the evidence outlined above, the variant was classified as pathogenic.
Mayo Clinic Laboratories, Mayo Clinic	RCV000494304	SCV002103271	pathogenic	not provided	2021-12-29	criteria provided, single submitter	clinical testing	PM5, PS3, PS4
Ambry Genetics	RCV002450742	SCV002739771	pathogenic	Cardiovascular phenotype	2022-10-20	criteria provided, single submitter	clinical testing	The p.D90N pathogenic mutation (also known as c.268G>A), located in coding exon 3 of the LDLR gene, results from a G to A substitution at nucleotide position 268. The aspartic acid at codon 90 is replaced by asparagine, an amino acid with highly similar properties. This alteration, also known as p.D69N, has been reported in multiple individuals with familial hypercholesterolemia (FH) and in FH cohorts from a variety of ethnic backgrounds (Day IN et al. Hum. Mutat., 1997;10:116-27; Mak YT et al. Arterioscler. Thromb. Vasc. Biol., 1998 Oct;18:1600-5; Khoo KL et al. Clin. Genet., 2000 Aug;58:98-105; Chang JH et al. J. Lipid Res., 2003 Oct;44:1850-8; Fouchier SW et al. Hum. Mutat., 2005 Dec;26:550-6; Norsworthy PJ et al. BMC Med. Genet., 2014 Jun;15:70). The results of functional studies demonstrated that protein product is retained in the endoplasmic reticulum and enzyme activity is reduced (Chang JH et al. J. Lipid Res., 2003 Oct;44:1850-8). Based on internal structural analysis, this alteration is considered to be deleterious, as it occurs in a known motif in a region of known function with an effect that matches known phenotype (Kurniawan ND et al. Protein Sci. 2000 Jul;9(7):1282-93). Several additional amino acid substitutions at this position have also been reported in individuals with FH, including D90A (Kolansky DM et al. Am. J. Cardiol., 2008 Dec;102:1438-43), D90E (Marduel M et al. Hum. Mutat., 2010 Nov;31:E1811-24), D90G (Hobbs HH et al. Hum. Mutat., 1992;1:445-66), and D90Y (Rubinsztein DC et al. Biochim. Biophys. Acta, 1993 Aug;1182:75-82). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV000238573	SCV002769529	pathogenic	Hypercholesterolemia, familial, 1	2020-10-19	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.2, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with familial hypercholesterolemia. (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance (Gene Reviews). (I) 0200 - Variant is predicted to result in a missense amino acid change from aspartic acid to asparagine (exon 3). (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (17 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a minor amino acid change. (SP) 0600 - Variant is located in the annotated calcium binding site of low-density lipoprotein receptor domain class A (NCBI). (I) 0701 - Other missense variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Four different variants in the same codon resulting in changes to tyrosine, alanine, glutamic acid and glycine have all been shown to cause familial hypercholesterolemia (ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. The variant has been previously reported in patients with familial hypercholesterolemia (ClinVar, PMID: 30649024). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Functional studies using COS7 cells show that this variant causes retention in the endoplasmic reticulum and reduction in LDLR activity (PMID: 12837857). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Revvity Omics, Revvity	RCV000238573	SCV003827191	pathogenic	Hypercholesterolemia, familial, 1	2022-06-28	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000494304	SCV004242963	pathogenic	not provided	2024-02-06	criteria provided, single submitter	clinical testing
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	RCV000238573	SCV000606056	pathogenic	Hypercholesterolemia, familial, 1		no assertion criteria provided	research
Clinical Genetics, Academic Medical Center	RCV000494304	SCV002034510	pathogenic	not provided		no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000494304	SCV002034885	pathogenic	not provided		no assertion criteria provided	clinical testing