rs875989909

chr19-11107486-C-G

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000527.5(LDLR):c.912C>G(p.Asp304Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000617 in 1,457,534 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D304H) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000062 (0 hom.)
• Consequence: LDLR NM_000527.5 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:13
• Conservation: PhyloP100: 0.650

Genes affected

LDLR (HGNC:6547): (low density lipoprotein receptor) The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. The encoded protein is normally bound at the cell membrane, where it binds low density lipoprotein/cholesterol and is taken into the cell. Lysosomes release the cholesterol, which is made available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the rate-limiting step in cholesterol synthesis. At the same time, a reciprocal stimulation of cholesterol ester synthesis takes place. Mutations in this gene cause the autosomal dominant disorder, familial hypercholesterolemia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2022]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a hotspot region, there are 13 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 11 uncertain in NM_000527.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr19-11107484-G-C is described in ClinVar as [Uncertain_significance]. Clinvar id is 440612.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, Uncertain_significance=1}.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.992
• PP5: Variant 19-11107486-C-G is Pathogenic according to our data. Variant chr19-11107486-C-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 226336.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr19-11107486-C-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5	c.912C>G	p.Asp304Glu	missense_variant	6/18	ENST00000558518.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6	c.912C>G	p.Asp304Glu	missense_variant	6/18	1	NM_000527.5	P3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000617 AC: 9 AN: 1457534 Hom.: 0 Cov.: 32 AF XY: 0.00000690 AC XY: 5 AN XY: 725050

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000811

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:13

Revision: reviewed by expert panel

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:7

Likely pathogenic, reviewed by expert panel	curation	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	Apr 05, 2022	The NM_000527.5(LDLR):c.912C>G (p.Asp304Glu) variant is classified as Likely pathogenic for Familial Hypercholesterolemia by applying evidence codes PM2, PP3, PM5, PS4_supporting, 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: PM2 - This variant is absent from gnomAD (gnomAD v2.1.1), so PM2 is Met. PP3 - REVEL = 0.871. It is above 0.75, so PP3 is Met. PM5 - 4 other missense variants in the same codon: - NNM_000527.5(LDLR):c.910G>A (p.Asp304Asn) (ClinVar ID 3692) - Pathogenic by these guidelines - NM_000527.5(LDLR):c.910G>C (p.Asp304His) (ClinVar ID 440612) - VUS by these guidelines - NM_000527.5(LDLR):c.911A>T (p.Asp304Val) (ClinVar ID 440613) - VUS by these guidelines - NM_000527.5(LDLR):c.910G>T (p.Asp304Tyr) (ClinVar ID 251517) - Likely pathogenic by these guidelines There is 1 variant in the same codon classified as Pathogenic by these guidelines, so PM5 is Met. PS4_supporting - Variant meets PM2 and is identified in at least 2 unrelated index cases: 1 index case who fulfils DLCN>6 criteria for FH from Robarts Research Institute and 1 index case who fulfils Simon Broome criteria for FH from MRC Clinical Sciences Centre, London UK (Tosi et al, 2007)(PMID: 17094996), so PS4_Supporting is Met. PP4 - Variant meets PM2 and is identified in at least 2 unrelated index cases as described in PS4, PP4 is Met. -
Likely pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Pathogenic, no assertion criteria provided	clinical testing	Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital	Jun 10, 2008	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Feb 11, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	Mar 30, 2017	- -
Likely pathogenic, 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	Dec 16, 2016	subject mutated among 2600 FH index cases screened = 1 / FH-Baltimore-1, 2 to 5% LDLR Activity / Software predictions: Benign -
Likely pathogenic, criteria provided, single submitter	clinical testing	Robarts Research Institute, Western University	Jan 02, 2018	- -

Familial hypercholesterolemia Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 16, 2017	Variant summary: The LDLR c.912C>G (p.Asp304Glu) variant involves the alteration of a non-conserved nucleotide that leads to the substitution of a highly conserved Asp in the ligand-binding region of the LDLR, in the class A repeat 7 domain (Interpro) where it is part of a highly conserved acidic residue motif (DXXXDXXDXXDE), corresponding to the 3rd conserved acidic residue that is involved in the proper folding of the domain through the coordinated binding of a calcium ion (Guo 2004). The variant was shown to result in a class 2B disease mechanism, i.e. causing a partial transport defect, where the LDLR protein is not properly transported from the endoplasmic reticulum to the Golgi apparatus for expression on the cell surface (Hobbs 1992). 4/5 in silico tools also predict a damaging outcome for this variant. This variant is absent in 246114 control chromosomes, but has been reported in several affected individuals (Hobbs 1992, Hooper 2012). In addition, multiple clinical diagnostic laboratories classified this variant as pathogenic/likely pathogenic. Taken together, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 04, 2024	This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 304 of the LDLR protein (p.Asp304Glu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 1301956, 17094996). This variant is also known as p.Asp283Glu. ClinVar contains an entry for this variant (Variation ID: 226336). 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: 1301956). This variant disrupts the p.Asp304 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17094996). 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. -
Likely pathogenic, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 22, 2020	The p.Asp304Glu variant in LDLR has been reported in 1 European and 1 Australian individual with familial hypercholesterolemia (PMID: 22883975, 1301956), and was absent from large population studies. This variant has also been reported in ClinVar as pathogenic and likely pathogenic (Variation ID: 226336). In vitro functional studies provide some evidence that the p.Asp304Glu variant may slightly impact protein function (PMID: 1301956). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. Two additional likely pathogenic variants, resulting in a different amino acid change at the same position, p.Asp304Tyr and p.Asp304Asn, have been reported in association with disease in the literature and Clinvar, supporting that a change at this position may not be tolerated (PMID: 17094996, 11845603, 1301956, 9664576, 21418584, 11810272, 12436241, 22698793, 11939787, 2088165/DOI: 10.1161/CIRCGEN.118.002192/Variation ID: 251517, 3692). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic. ACMG/AMP Criteria applied: PM2, PM5, PP3, PS3_supporting, PS4_supporting (Richards 2015). -

Homozygous familial hypercholesterolemia Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jan 19, 2018

The p.Asp304Glu variant in LDLR has been reported in at least 3 individuals with familial hypercholesterolemia, two of which were compound heterozygotes (FH; Ho bbs 1992, Tosi 2007, Webb 1996). It has also been reported by other clinical lab oratories in ClinVar (Variation ID 226336) and is absent from large population s tudies. In vitro functional studies have shown that cultured fibroblasts from co mpound heterozygous carriers of the p.Asp304Glu variant have reduced LDLR activ ity (2-5% with c.2309-?_*2514+?del and 25-30% with p.Asp96Gly; Hobbs 1992, Webb 1996). In addition, other disease-causing variants (p.Asp304Asn, p.Asp304Tyr) a t this position have been reported in individuals with FH (Hobbs 1992, Do 2015, Loux 1992, Thormaehlen 2015, Tichy 2012, Vohnout 2016), suggesting changes at th is position are not tolerated. In summary, although additional studies are requi red to fully establish its clinical significance, the p.Asp304Glu variant is lik ely pathogenic. ACMG/AMP Criteria applied: PM2, PM5, PS3_Moderate, PS4_Supportin g (Richards 2015). -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Oct 31, 2023

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.D283E and FH Baltimore-1; This variant is associated with the following publications: (PMID: 11313767, 22883975, 33087929, 31447099, 32041611, 33303402, 34037665, 2088165, 17094996, 1301956, 9026534) -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 05, 2021

The p.D304E pathogenic mutation (also known as c.912C>G), located in coding exon 6 of the LDLR gene, results from a C to G substitution at nucleotide position 912. The aspartic acid at codon 304 is replaced by glutamic acid, an amino acid with highly similar properties. This alteration has been reported, sometimes with p.D283E legacy nomenclature, in familial hypercholesterolemia (FH) cohorts (Heath KE et al. Eur. J. Hum. Genet. 2001;9:244-52; Hooper AJ et al. Atherosclerosis. 2012;224:430-4). It has also been detected in the compound heterozygous state in individuals with homozygous FH (Hobbs HH et al. Hum. Mutat. 1992;1:445-66; Webb JC et al. J. Lipid Res. 1996;37:368-81; Klaus G et al. Pediatr Nephrol, 2018 07;33:1199-1208). Fibroblasts from compound heterozygous patients exhibited reduced LDLR activity, but the impact of the p.D304E alteration alone was not investigated (Hobbs HH et al. Hum. Mutat. 1992;1:445-66; Webb JC et al. J. Lipid Res. 1996;37:368-81). Another alteration at the same codon, p.D304N (c.910G>A), has been detected in individuals with FH (Leitersdorf E et al. J. Clin. Invest., 1990;85:1014-23). This amino acid position is highly conserved in available vertebrate species. 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: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Pathogenic	0.50
Cadd	Benign	22
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.88	D;.;.;.;.;.
Eigen	Uncertain	0.29
Eigen_PC	Benign	0.15
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Pathogenic	0.97	D;D;D;D;D;D
M_CAP	Pathogenic	0.83	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	4.0	H;.;.;.;.;H
MutationTaster	Benign	1.0	D;D;D;D;D;D;D
PrimateAI	Uncertain	0.52	T
PROVEAN	Uncertain	-3.4	D;D;D;D;D;D
Sift	Uncertain	0.026	D;D;D;D;D;D
Sift4G	Benign	0.071	T;T;T;T;T;T
Polyphen		0.81	P;.;.;.;.;.
Vest4		0.85
MutPred		0.96		Gain of disorder (P = 0.165);Gain of disorder (P = 0.165);.;.;.;Gain of disorder (P = 0.165);
MVP		1.0
MPC		0.72
ClinPred		0.99	D
GERP RS		3.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.79
gMVP		0.98

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs875989909; hg19: chr19-11218162;