19-11116201-G-T

Position:

• chr19-11116201-G-T

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.1694G>T​(p.Gly565Val) 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G565A) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LDLR NM_000527.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:11
• Conservation: PhyloP100: 9.87

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 strand (size 6) in uniprot entity LDLR_HUMAN there are 17 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 chr19-11116201-G-C is described in Lovd as [Likely_pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.995
• PP5: Variant 19-11116201-G-T is Pathogenic according to our data. Variant chr19-11116201-G-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 3688.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11116201-G-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LDLR	NM_000527.5	c.1694G>T	p.Gly565Val	missense_variant	11/18	ENST00000558518.6	NP_000518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LDLR	ENST00000558518.6	c.1694G>T	p.Gly565Val	missense_variant	11/18	1	NM_000527.5	ENSP00000454071.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:11

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:8

Likely pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Nov 15, 2023	The c.1694G>T (p.Gly565Val) variant in LDLR gene, that encodes for low density lipoprotein receptor, has been identified in at least five individuals who fulfill the clinical criteria of Familial Hypercholesterolemia (FH) (PMID:12436241, 23375686, 32770674, 28161202). This variant has also been reported in homozygous/compound heterozygous (with p.Trp4*) status in individuals with severe FH (PMID: 27784735, 6299582). This variant has also been detected in hypercholesterolemia cohorts and cohorts referred for FH testing (PMID: 34037665, 34297352). Experimental studies on transfected CHO cells demonstrated that this variant caused complete retention of protein on the endoplasmic reticulum, severely affected LDLR surface expression, and no LDL particle internalization (PMID: 16740646, 16257961). In addition, studies on homozygous mutant cells showed LDLR activity of <2% compared to wild type (PMID: 1301956, 2901412, 6299582). In-silico computational prediction tools suggest that this variant may have deleterious effect on the protein function (REVEL score: 0.971). This variant is found to be absent in the general population database, gnomAD and interpreted as likely pathogenic/pathogenic by several submitters (10) in the ClinVar database (ClinVar ID: 3688). Other amino acid substitutions at the same codon (p.Gly565Arg, p.Gly565Asp, p.Gly565Ala) have been reported in individuals with FH (PMID: 33994402, 27784735, 11313767) and classified as likely pathogenic by ClinVar submitters (ClinVar ID: 1778186, 375819, 226366). Therefore, the c.1694G>T (p.Gly565Val) variant in LDLR gene is classified as likely pathogenic. -
Pathogenic, criteria provided, single submitter	curation;literature only	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	Mar 01, 2016	- -
Pathogenic, no assertion criteria provided	research	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	Mar 30, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory of molecular diagnosis of dyslipidemias, Università egli studi di Napoli Federico II	May 24, 2021	- -
Likely pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Sep 15, 1988	- -
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	subjects mutated among 2600 FH index cases screened = 6 , family members = 2 with co-segregation / Functional test, FH-Naples-2, 2% LDLR Activity, Other mutations at same codon / Software predictions: Damaging -

Homozygous familial hypercholesterolemia Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jan 09, 2020

The p.Gly565Val variant in LDLR (also described as p.Gly544Val in the literature) has been reported in the heterozygous state in at least 5 individuals and in the homozygous state in 1 individual with familial hypercholesterolemia (FH) and segregated with disease in 2 affected relatives from at least one family (ClinVar: SCV000503387.1 and SCV000583865.1, Esser 1988, Amsellem 2002). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID: 3688) and was absent from large population studies. Computational prediction tools and conservation analyses suggest that this variant may impact the protein. In vitro functional studies support an impact on protein function (Esser 1988). Additional variants involving this codon (p.Gly565Asp and p.Gly565Ala) have been identified in individuals with FH. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant FH. ACMG/AMP Criteria applied: PM2, PS4_Moderate, PP3, PS3_Supporting -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 26, 2022

The p.G565V pathogenic mutation (also known as c.1694G>T), located in coding exon 11 of the LDLR gene, results from a G to T substitution at nucleotide position 1694. The glycine at codon 565 is replaced by valine, an amino acid with dissimilar properties. This variant (also referred to as p.G544V) has been detected in individuals reported to have homozygous or heterozygous familial hypercholesterolemia (FH), and assays on homozygous patient cells reportedly showed LDLR activity of <2% compared to wild type (Esser V et al. J Biol Chem, 1988 Sep;263:13276-81; Hobbs HH et al. Hum Mutat, 1992;1:445-66; Amsellem S et al. Hum Genet, 2002 Dec;111:501-10; Rieck L et al. Clin Genet, 2020 11;98:457-467). This variant was also detected in additional hypercholesterolemia cohorts and cohorts referred for FH testing (Bertolini S et al. Atherosclerosis, 2013 Apr;227:342-8; Di Taranto MD et al. Clin Genet, 2021 11;100:529-541; Sturm AC et al. JAMA Cardiol, 2021 08;6:902-909). Several In vitro studies indicate that this variant results in LDLR protein that is retained in the endoplasmic reticulum, not reaching the plasma membrane (Esser V et al. J Biol Chem, 1988 Sep;263:13276-81; Tveten K et al. FEBS J, 2007 Apr;274:1881-93; Oka OB et al. Mol Cell, 2013 Jun;50:793-804; Du&scaron;kov&aacute; L et al. Front Genet, 2020 Jun;11:691; Lebeau PF et al. J Clin Invest, 2021 01;131). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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. -

Familial hypercholesterolemia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Apr 11, 2022

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Gly565 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been observed in individuals with LDLR-related conditions (PMID: 11313767, 27784735), which suggests that this may be a clinically significant amino acid residue. Experimental studies have shown that this missense change affects LDLR function (PMID: 2901412, 16740646). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 3688). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 2901412, 12436241, 23375686). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 565 of the LDLR protein (p.Gly565Val). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.59	D
BayesDel_noAF	Pathogenic	0.61
CADD	Pathogenic	31
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.93	D;.;.;.;.;.
Eigen	Pathogenic	0.94
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.99	D;D;D;D;D;D
M_CAP	Pathogenic	0.89	D
MetaRNN	Pathogenic	1.0	D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.4	H;.;.;.;.;H
PrimateAI	Uncertain	0.69	T
PROVEAN	Pathogenic	-8.4	D;D;D;D;D;D
REVEL	Pathogenic	0.97
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		0.92
MutPred		0.97		Loss of catalytic residue at L570 (P = 0.1586);Loss of catalytic residue at L570 (P = 0.1586);.;.;.;Loss of catalytic residue at L570 (P = 0.1586);
MVP		1.0
MPC		0.91
ClinPred		1.0	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.99
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: rs28942082; hg19: chr19-11226877;