19-11102772-A-T

Position:

• chr19-11102772-A-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.299A>T​(p.Asp100Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,144 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. D100G) has been classified as Likely pathogenic.

• Frequency: Genomes: 𝑓 0.0000066 (0 hom., cov: 31)
• Consequence: LDLR NM_000527.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:7 U:2
• Conservation: PhyloP100: 9.28

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]

LDLR (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a domain LDL-receptor class A 2 (size 40) in uniprot entity LDLR_HUMAN there are 46 pathogenic changes around while only 6 benign (88%) 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 chr19-11102772-A-G is described in Lovd as [Likely_pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.996
• PP5: Variant 19-11102772-A-T is Pathogenic according to our data. Variant chr19-11102772-A-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 369854.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LDLR	NM_000527.5	c.299A>T	p.Asp100Val	missense_variant	3/18	ENST00000558518.6	NP_000518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LDLR	ENST00000558518.6	c.299A>T	p.Asp100Val	missense_variant	3/18	1	NM_000527.5	ENSP00000454071.1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152144 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152144 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 74320

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:7 Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:2 Uncertain:1

Uncertain significance, flagged submission	clinical testing	Robarts Research Institute, Western University	Aug 22, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jan 01, 2019	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Apr 13, 2023	- -

Familial hypercholesterolemia Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Sep 20, 2023	This missense variant replaces aspartic acid with valine at codon 100 in the LDLR type A repeat 2 of the LDLR protein. This variant is also known as p.Asp79Val 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). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in multiple unrelated individuals affected with familial hypercholesterolemia (PMID: 11381031, 27765764, 28964736, 32143996, 34040191, 34407635; Color internal data; ClinVar SCV000484769.2) and has been shown to segregate with hypercholesterolemia phenotype in 3 members of one family (PMID: 11381031). It has also been reported in an individual affected with early-onset myocardial infarction (PMID: 30586733). This variant has been identified in 1/31394 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different variants affecting the same codon, p.Asp100Asn and p.Asp100Gly, are considered to be disease-causing (ClinVar variation ID: 251121, 251122), suggesting that aspartic acid at this position is important for LDLR protein function. Based on the available evidence, this variant is classified as Likely Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 24, 2023	This sequence change replaces aspartic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 100 of the LDLR protein (p.Asp100Val). This variant is present in population databases (no rsID available, gnomAD 0.007%). This missense change has been observed in individuals with clinical features of familial hypercholesterolemia and/or early-onset myocardial infarction (PMID: 27765764, 28964736, 30586733; Invitae). ClinVar contains an entry for this variant (Variation ID: 369854). 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%. This variant disrupts the p.Asp100 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been observed in individuals with LDLR-related conditions (PMID: 25936346), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:1 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 19, 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.(D79V); This variant is associated with the following publications: (PMID: 28964736, 34040191, 27765764, 30586733, 32143996, 12827279, 34407635, 11381031) -
Uncertain significance, flagged submission	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Aug 11, 2016	Genetic testing: The patient had genetic testing for the familial hypercholesterolemia panel. The test included sequencing of three genes associated with familial hypercholesterolemia: LDLR, APOB and PCSK9 and deletion/duplication analysis for the LDLR gene. p.Asp200Val (c.299A>T) in the LDLR gene (NM_000527.4) The lab classifies this variant as a variant, likely pathogenic. Given a lack of case data for this specific variant, in combination with in-silico tools and the knowledge that there are two other pathogenic variants that have been identified at this amino acid (D100N and D100E) we consider this variant of unknown significance, but likely pathogenic and we do feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing") in combination with a full lipid panel. The specific variant has not been reported before in individuals with familial hypercholesterolemia (not including this patient's family). However, two other variants have been seen at the same amino acid (D100N and D100E). Both of these changes are listed as pathogenic. This change falls within a turn motif of the protein that includes amino acids 99-103. The native, acidic aspartic acid at the 100th aa position is substituted by a valine which is hydrophobic and small in size. The other two variants that have been found at this position include substitutions with a an amide of similar structure (D100N) and a glutamic acid which has a larger structure and an acidic nature (D100E). In silico analysis with PolyPhen-2 predicts the variant to be pathogenic (HumVar: 1.00) as does mutation taster (0.999). The aspartic acid at codon 100 is conserved across species. There is no variation at codon 100 listed in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), which currently includes variant calls on ~64,000 individuals of European, African, Latino and Asian descent (as of August 11, 2016). The average coverage at that site in ExAC is 30x. -

LDLR-related disorder Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 21, 2023

The LDLR c.299A>T variant is predicted to result in the amino acid substitution p.Asp100Val. This variant was reported in three individuals with myocardial infarction/familial hypercholesterolemia (Table 1, Khera et al 2019. PubMed ID: 30586733; Table S2, Ajufo E et al 2021. PubMed ID: 34040191; Table, Björnsson E et al 2021. PubMed ID: 34407635). Different variants affecting the same amino acid (p.Asp100Asn, p.Asp100Gly, and p.Asp100Gly) were reported to be associated with familial hypercholesterolemia (Human Gene Mutation Database). In ClinVar, this variant is interpreted as uncertain/likely pathogenic/pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/369854/?new_evidence=true). This variant is reported in 0.0065% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/19-11213448-A-T). In summary, this variant is interpreted as likely pathogenic. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 12, 2022

The p.D100V pathogenic mutation (also known as c.299A>T), located in coding exon 3 of the LDLR gene, results from an A to T substitution at nucleotide position 299. The aspartic acid at codon 100 is replaced by valine, an amino acid with highly dissimilar properties. This alteration impacts a residue in the conserved cluster of acidic amino acids (consensus sequence DCXDXSDE) at the C-terminal end of LDLR class A repeat 2 (Jeon H and Blacklow C. Annu. Rev. Biochem. 2005;74:535-62). This variant has been reported in several familial hypercholesterolemia (FH) cohorts (Wang J et al. Arterioscler. Thromb. Vasc. Biol. 2016;36:2439-2445; Defesche JC et al. J Clin Lipidol. 2017;11:1338-1346.e7). In addition, two other likely pathogenic alterations, p.D100E and p.D100N, have been described in the same codon (Klanar G et al. J Am Coll Cardiol. 2015;66:1250-7; Leren TP et al. Semin Vasc Med. 2004;4:75-85). 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	1.0
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Pathogenic	0.60
CADD	Uncertain	25
DANN	Uncertain	0.98
DEOGEN2	Pathogenic	0.96	D;.;.;.;.
Eigen	Pathogenic	0.79
Eigen_PC	Uncertain	0.57
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.99	D;D;D;D;D
M_CAP	Pathogenic	0.96	D
MetaRNN	Pathogenic	1.0	D;D;D;D;D
MetaSVM	Pathogenic	0.96	D
MutationAssessor	Pathogenic	4.4	H;.;H;H;H
PrimateAI	Benign	0.36	T
PROVEAN	Pathogenic	-8.1	D;D;D;D;D
REVEL	Pathogenic	0.88
Sift	Pathogenic	0.0	D;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D
Polyphen		1.0	D;.;.;.;.
Vest4		0.90
MutPred		0.90		Loss of loop (P = 0.1258);Loss of loop (P = 0.1258);Loss of loop (P = 0.1258);Loss of loop (P = 0.1258);Loss of loop (P = 0.1258);
MVP		1.0
MPC		0.98
ClinPred		1.0	D
GERP RS		5.7
RBP_binding_hub_radar		0.97
RBP_regulation_power_radar		2.0
Varity_R		0.99
gMVP		1.0

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: rs879254460; hg19: chr19-11213448;