19-11116888-G-A

Position:

• chr19-11116888-G-A

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1 PM2 PM5 PP3_Strong PP5

The NM_000527.5(LDLR):​c.1735G>A​(p.Asp579Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D579A) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LDLR NM_000527.5 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:1
• Conservation: PhyloP100: 8.00

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 11 ACMG points.

• PM1: In a strand (size 5) in uniprot entity LDLR_HUMAN there are 21 pathogenic changes around while only 0 benign (100%) 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 chr19-11116889-A-C is described in Lovd as [Likely_pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.995
• PP5: Variant 19-11116888-G-A is Pathogenic according to our data. Variant chr19-11116888-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 252006.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Pathogenic=4, Likely_pathogenic=2}. Variant chr19-11116888-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LDLR	NM_000527.5	c.1735G>A	p.Asp579Asn	missense_variant	12/18	ENST00000558518.6	NP_000518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LDLR	ENST00000558518.6	c.1735G>A	p.Asp579Asn	missense_variant	12/18	1	NM_000527.5	ENSP00000454071.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Oct 19, 2018	Across a selection of available literature, the LDLR c.1735G>A (p.Asp579Asn) variant, also known as p.Asp558Asn, has been reported in at least five studies and is found in at least seven probands with familial hypercholesterolemia in a heterozygous state (Hobbs et al. 1992; Ekstrom et al. 1995; Vuorio et al. 2001; Brusgaard et al. 2006). Control data are unavailable for this variant and it is not found in the 1000 Genomes Project, the Exome Sequencing Project, the Exome Aggregation Consortium or the Genome Aggregation Database, with good sequence coverage of this region, and therefore it is presumed to be rare. Functional studies in cultured proband fibroblasts demonstrated that the p.Asp579Asn variant protein had 52% LDL binding, 42% internalization, and 46% degradation compared to control fibroblasts, suggesting that it had a binding-defective phenotype (Vuorio et al. 2001). Expression analysis in proband fibroblasts also found p.Asp579Asn to have 2% LDL receptor activity compared to controls (Hobbs et al. 1992). The Asp579 residue is highly conserved across species and x-ray crystallography demonstrated the importance of the Asp579 residue in hydrogen bonding necessary for structural formation (Ekstrom et al. 1995; Jeon et al. 2001). Based on the evidence, the p.Asp579Asn variant is classified as pathogenic for familial hypercholesterolemia. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Likely pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -

not provided Pathogenic:1 Uncertain:1

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Oct 21, 2019	Not found in the gnomAD exomes dataset, and the data is high quality. This variant is statistically more frequent in affected individuals than in the general population and/or healthy controls. Found in at least one patient with expected phenotype for this gene. Predicted to have a damaging effect on the protein. Other pathogenic or likely pathogenic variants affect the same amino acid. Assessment of experimental evidence suggests this variant results in abnormal protein function. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Apr 25, 2022	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; Published functional studies show that cultured fibroblasts from a patient with p.(D579N) and another unknown LDLR variant had <2% LDLR activity (Hobbs et al., 1992); however, the p.(D579N) variant was not studied in isolation and its functional effect in vivo is unknown; Also known as D558N, FH-Cincinnati-4; This variant is associated with the following publications: (PMID: 10532689, 11373616, 28965616, 7635461, 34037665, 31447099, 29874871, 31689621, 31401775, 11585102, 1301956, 16542394, 33955087) -

Homozygous familial hypercholesterolemia Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

May 04, 2018

The p.Asp579Asn variant (also known as p.Asp558Asn, FH-Cinncinatti-4) in LDLR ha s been reported in 7 individuals with hypercholesterolemia (5 heterozygous, 1 do uble heterozygote with the p.Arg3527Gln variant in APOB, and one individual desc ribed by the authors as "compound heterozygote with an unidentified second varia nt"; Hobbs 1992, Ekstrom 1995, Jensen 1999, Brusgaard 2006, Pirillo 2017). This variant was absent from large population studies and is reported in ClinVar (Var iation ID: 252006). In vitro functional studies provide some evidence that the p .Asp5789Asn variant may result in transport defects and ER retention of the LDL receptor (Hobbs 1992). However, these types of assays may not accurately represe nt biological function. Computational prediction tools and conservation analysis suggest that the p.Asp579Asn variant may impact the protein, though this inform ation is not predictive enough to determine pathogenicity. A different variant a t the same residue (p.Asp579Tyr) has been identified in >15 Italian individuals with hypercholesterolemia, suggesting change at this position may not be tolerat ed (Bertolini 2000). In summary, although additional studies are required to ful ly establish its clinical significance, the p.Asp579Asn variant is likely pathog enic. ACMG/AMP Criteria applied: PM2; PM5; PS4_Moderate; PP3; PS3_Supporting. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 16, 2022

The p.D579N pathogenic mutation (also known as c.1735G>A), located in coding exon 12 of the LDLR gene, results from a G to A substitution at nucleotide position 1735. The aspartic acid at codon 579 is replaced by asparagine, an amino acid with highly similar properties. This variant (also referred to as p.D558N) has been detected in the heterozygous, compound heterozygous, and homozygous states in individuals with definite or suspected heterozygous familial hypercholesterolemia (FH) and homozygous FH, as well as in individuals from FH cohorts and cohorts referred for FH genetic testing (Hobbs HH et al. Hum Mutat, 1992;1:445-66; Ekström U et al. Hum Genet, 1995 Aug;96:147-50; Jensen HK et al. Clin Genet, 1996 Nov;50:388-92; Vuorio AF et al. Ann Med, 2001 Sep;33:410-21; Brusgaard K et al. Clin Genet, 2006 Mar;69:277-83; Di Taranto MD et al. Clin Genet, 2021 11;100:529-541; Benedek P et al. J Intern Med, 2021 08;290:404-415; Sturm AC et al. JAMA Cardiol, 2021 08;6:902-909). In addition, assays performed on cell lines from individuals with this variant demonstrated reduced protein function (Jensen HK et al. Clin Genet, 1996 Nov;50:388-92; Vuorio AF et al. Ann Med, 2001 Sep;33:410-21). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Familial hypercholesterolemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 20, 2022

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Asp558 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10978268, 23375686). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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. ClinVar contains an entry for this variant (Variation ID: 252006). This variant is also known as p.Asp558Asn. This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 1301956, 16542394). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 579 of the LDLR protein (p.Asp579Asn). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	0.11
CADD	Pathogenic	31
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.94	D;.;.;.;.;.
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	1.0	D;D;D;D;D;D
M_CAP	Pathogenic	0.95	D
MetaRNN	Pathogenic	1.0	D;D;D;D;D;D
MetaSVM	Pathogenic	0.98	D
MutationAssessor	Pathogenic	4.1	H;.;.;.;.;H
PrimateAI	Uncertain	0.61	T
PROVEAN	Pathogenic	-4.8	D;D;D;D;D;D
REVEL	Pathogenic	0.85
Sift	Pathogenic	0.0	D;D;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D
Polyphen		1.0	D;.;.;.;.;.
Vest4		0.95
MutPred		0.98		Gain of loop (P = 0.0312);Gain of loop (P = 0.0312);.;.;.;Gain of loop (P = 0.0312);
MVP		1.0
MPC		0.80
ClinPred		1.0	D
GERP RS		5.5
Varity_R		0.96
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.17		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: rs875989929; hg19: chr19-11227564;