Submissions for variant NM_000527.5(LDLR):c.1195G>A (p.Ala399Thr)

gnomAD frequency: 0.00001  dbSNP: rs730882099

Total submissions: 14

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
LDLR-LOVD, British Heart Foundation	RCV000237472	SCV000295288	likely pathogenic	Hypercholesterolemia, familial, 1	2016-03-25	criteria provided, single submitter	literature only
Labcorp Genetics (formerly Invitae), Labcorp	RCV001211912	SCV001383476	pathogenic	Familial hypercholesterolemia	2023-10-30	criteria provided, single submitter	clinical testing	This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 399 of the LDLR protein (p.Ala399Thr). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individuals with hypercholesterolemia (PMID: 10634824, 15241806, 16250003, 16343504, 21925044, 23375686, 26723464, 32977124). ClinVar contains an entry for this variant (Variation ID: 183109). 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 does not substantially affect LDLR function (PMID: 32015373). This variant disrupts the p.Ala399 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been observed in individuals with LDLR-related conditions (PMID: 21382890), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.
Institute of Human Genetics, University of Leipzig Medical Center	RCV000237472	SCV001440417	uncertain significance	Hypercholesterolemia, familial, 1	2019-01-01	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV001800473	SCV002046305	likely pathogenic	not specified	2020-10-21	criteria provided, single submitter	clinical testing	This variant has been reported in individuals affected with familial hypercholesterolemia (FH) in the published literature (PMIDs: 10634824 (2000), 15241806 (2004), 16250003 (2005), 23375686 (2013), and 26723464 (2016)). 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 disease causing and damaging. A different variant located as the same amino acid posistion has been described as likely pathogenic and pathogenic. Based on the available information, the variant is predicted to be likely pathogenic.
3billion	RCV000237472	SCV002521646	likely pathogenic	Hypercholesterolemia, familial, 1	2022-05-22	criteria provided, single submitter	clinical testing	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.002%). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.76; 3Cnet: 0.98). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000183109). A different missense change at the same codon (p.Ala399Asp) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000226350). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.
Ambry Genetics	RCV002336376	SCV002643753	uncertain significance	Cardiovascular phenotype	2024-06-13	criteria provided, single submitter	clinical testing	The p.A399T variant (also known as c.1195G>A), located in coding exon 9 of the LDLR gene, results from a G to A substitution at nucleotide position 1195. The alanine at codon 399 is replaced by threonine, an amino acid with similar properties, and is located in the EGF precursor-like domain. This variant (also described as p.A378T and FH-Nuoro) has been reported in multiple individuals from a variety of ethnic backgrounds with familial hypercholesterolemia (FH), including heterozygotes, compound heterozygotes, and homozygous cases; it has also been reported in one case and one control from a myocardial infarction cohort (Deiana L et al. Arterioscler. Thromb. Vasc. Biol., 2000 Jan;20:236-43; Bertolini S et al. Atherosclerosis, 2013 Apr;227:342-8; Thormaehlen AS et al. PLoS Genet., 2015 Feb;11:e1004855; Sánchez-Hernández RM et al. Circ Cardiovasc Genet, 2016 Dec;9:504-510; Chiou KR et al. J Clin Lipidol 2017 Jan;11:386-393.e6). Functional studies in cultured skin fibroblasts have demonstrated conflicting results, with some suggesting reduced LDL receptor activity and others showing no significant difference from wild-type LDL binding and receptor activity (Deiana L et al. Arterioscler. Thromb. Vasc. Biol., 2000 Jan;20:236-43; Pisciotta L et al. Atherosclerosis, 2006 Oct;188:398-405; Thormaehlen AS et al. PLoS Genet., 2015 Feb;11:e1004855; Galicia-Garcia U et al. Sci Rep, 2020 02;10:1727). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear.
GeneDx	RCV000161981	SCV003798746	uncertain significance	not provided	2023-01-30	criteria provided, single submitter	clinical testing	Identified in individuals with premature coronary artery disease (CAD) and early myocardial infarction (MI) in the published literature (Anderson et al., 2010; Do et al., 2015); Not observed at a significant frequency in large population cohorts (gnomAD); Published functional studies show protein expression, receptor binding, and LDL uptake similar to wild type protein (Galicia-Garcia et al., 2020); In silico analysis supports that this missense variant does not alter protein structure/function; Also known as A378T or FH-Nuoro; This variant is associated with the following publications: (PMID: 15241806, 21925044, 10634824, 16250003, 16343504, 20691829, 25647241, 27050191, 27784735, 28502495, 26723464, Giammanco_2022_Abstract, 32977124, 34037665, 35339733, 33994402, 25487149, 32015373, 23375686)
New York Genome Center	RCV000237472	SCV003925392	likely pathogenic	Hypercholesterolemia, familial, 1	2022-01-28	criteria provided, single submitter	clinical testing	The c.1195G>A p.(Ala399Thr) variant identified in the LDLR gene substitutes a well conserved Alanine for Threonine at amino acid 399/860 (exon9/18). This variant is found with low frequency in gnomAD(v3.1.2)(1 heterozygote, 0 homozygote; allele frequency: 6.579e-6), suggesting it is not a common benign variant in the populations represented in that database. In silico algorithms predict this variant to be deleterious (CADD score = 26.2, REVEL score = 0.755) to the function of the canonical transcript. This variant is reported in ClinVar as Likely Pathogenic (n=3) and as a Variant of Uncertain Significance (n=1) (VarID:183109) and has been reported in many affected individuals in the literature [PMID: 10978268, 15241806, 21925044, others]. Given its presence in many affected individuals in the literature, low frequency in population databases, and in silico predictions of a damaging effect to protein function, the c.1195G>A p.(Ala399Thr) variant identified in the LDLR gene is reported as Likely Pathogenic.
Color Diagnostics, LLC DBA Color Health	RCV001211912	SCV004358513	likely pathogenic	Familial hypercholesterolemia	2023-06-13	criteria provided, single submitter	clinical testing	This missense variant (also known as p.Ala378Thr in the mature protein) replaces alanine with threonine in the type B repeat 1 at codon 399 of the LDLR 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). Experimental functional studies for this variant have shown conflicting results. In two different transfected cell assays, this variant showed normal LDLR activity (PMID: 25647241, 32015373). Another study using fibroblasts derived from a homozygous individual affected with a severe phenotype showed a significant reduction in LDL receptor activity (PMID: 16343504). This LDLR variant has been reported in multiple heterozygous individuals affected with familial hypercholesterolemia (PMID: 16250003, 21925044, 23833242, 28502495, 33994402). This variant has also been observed in both compound heterozygous state with a known pathogenic LDLR variant and in homozygosity in several individuals affected with severe homozygous familial hypercholesterolemia, a phenotype expected of having two deleterious LDLR variants (PMID: 23375686, 27784735, 28432645, 32977124). Additionally, this variant has been reported in an individual affected with myocardial infarction (PMID: 25487149) and in an individual affected with coronary artery disease (PMID: 27050191). This variant has been identified in 5/245772 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001211912	SCV005076120	pathogenic	Familial hypercholesterolemia	2024-04-16	criteria provided, single submitter	clinical testing	Variant summary: LDLR c.1195G>A (p.Ala399Thr) 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 1.6e-05 in 250750 control chromosomes. c.1195G>A has been reported in the literature in multiple individuals affected with Autosomal Recessive Familial Hypercholesterolemia (examples, Bertolini_2013, DErasmo_2017, Sanchez-Hernandez_2016 ). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. These results showed no damaging effect of this variant on LDL-uptake function in a cellular model (Thormaehlen_2015). Additionally, at least one variant at the p.Ala399 residue has been reported as associated with disease (p.Ala399Asp), suggesting that this codon is functionally important. The following publications have been ascertained in the context of this evaluation (PMID: 23375686, 28432645, 27784735, 25647241). ClinVar contains an entry for this variant (Variation ID: 183109). Based on the evidence outlined above, the variant was classified as pathogenic.
Juno Genomics, Hangzhou Juno Genomics, Inc	RCV000237472	SCV005417655	likely pathogenic	Hypercholesterolemia, familial, 1		criteria provided, single submitter	clinical testing	PM2_Supporting+PP3+PS4
Dept. of Genetics and Pharmacogenomics, Merck Research Labs	RCV000161981	SCV000189556	not provided	not provided		no assertion provided	in vitro
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	RCV000237472	SCV000606351	pathogenic	Hypercholesterolemia, familial, 1		no assertion criteria provided	research
Natera, Inc.	RCV001211912	SCV002086412	likely pathogenic	Familial hypercholesterolemia	2020-08-10	no assertion criteria provided	clinical testing