rs875989906

Variant names:

• chr19-11105567-G-A
• rs875989906
• NM_000527.5:c.661G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-11105567-G-A
• chr19-11105567-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.661G>A​(p.Asp221Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000617 in 1,459,316 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. D221G) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000062 (0 hom.)
• Consequence: LDLR NM_000527.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:18
• Conservation: PhyloP100: 9.88

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 disulfide_bond (size 15) in uniprot entity LDLR_HUMAN there are 56 pathogenic changes around while only 2 benign (97%) 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 chrnull-null-null-null is described in UniProt as null.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.994
• PP5: Variant 19-11105567-G-A is Pathogenic according to our data. Variant chr19-11105567-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 226331.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-11105567-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LDLR	NM_000527.5	c.661G>A	p.Asp221Asn	missense_variant	Exon 4 of 18	ENST00000558518.6	NP_000518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDLR	ENST00000558518.6	c.661G>A	p.Asp221Asn	missense_variant	Exon 4 of 18	1	NM_000527.5	ENSP00000454071.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000617 AC: 9 AN: 1459316 Hom.: 0 Cov.: 33 AF XY: 0.00000689 AC XY: 5 AN XY: 725566

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000190

Gnomad4 NFE exome AF: 0.00000630

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:18

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:10

Jun 05, 2019

Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Mar 25, 2016

LDLR-LOVD, British Heart Foundation

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: literature only

- -

Apr 15, 2024

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PS4,PM5_STR,PM2_SUP,PP3 -

Jun 09, 2024

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.661G>A (p.Asp221Asn) variant (also known as p.Asp200Asn) in the LDLR gene, that encodes for low density lipoprotein receptor, has been identified in numerous individuals (>100) affected with Familial Hypercholesterolemia (FH) (PMID: 17094996, 9409298, 25962062, 29399563, 33740630, 17142622, 15199436). This variant has also been reported in homozygous status in an individual with severe FH (total cholesterol >500mg/dL, LDL-C: Unknown) (PMID: 22836070). Experimental studies using patient-derived lymbhoblasts revealed reduced LDLR activity (PMID: 9409298). This variant is located within the well-established LDL binding domain (amino acids 105-232) critical for protein function (PMID: 2600087). Computational prediction tools suggest that the p.Asp221Asn variant may have deleterious effect on the protein function (REVEL score: 0.816). This variant is found to be rare (9/1459316; 0.0006167%) in the general population database, gnomAD v4.0.0 and interpreted as pathogenic by multiple submitters in ClinVar (ID: 226331). Other substitutions affecting the same amino acid position, p.Asp221Tyr (ClinVar ID: 251356) and p.Asp221Gly (ClinVar ID: 183092), have also been reported to be pathogenic by the ClinGen variant curation expert panel. Therefore, the c.661G>A (p.Asp221Asn) variant in LDLR gene is classified as pathogenic. -

Dec 16, 2016

Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

subject mutated among 2600 FH index cases screened = 1 / previously described in association with FH / Software predictions: Conflicting -

Nov 05, 2016

Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Asp221 bind structural Ca2+. -

-

Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Jun 27, 2008

Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Apr 04, 2023

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 11, 2024

Institute of Human Genetics, Heidelberg University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Familial hypercholesterolemia Pathogenic:5

May 12, 2023

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant (also known as p.Asp200Asn in the mature protein) replaces aspartic acid with asparagine at codon 221 in the LDLR type A repeat 5 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 have shown that this variant may disrupt LDLR protein folding due to defective calcium ion binding (PMID: 8784348, 9262405) and result in reduced LDLR activity (PMID: 9409298). This variant has been reported in over 100 individuals affected with familial hypercholesterolemia (PMID: 9409298, 10090484, 11196104, 16250003, 17094996, 24075752, 25962062, 29399563, 33740630, 34456200). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Different missense variants affecting the same codon (p.Asp221Gly, p.Asp221Tyr, Asp221Val) are considered to be disease-causing (ClinVar variation ID: 183092, 251356, 251357), suggesting that aspartic acid at this position is important for LDLR protein function. Based on the available evidence, this variant is classified as Pathogenic. -

Nov 30, 2020

Natera, Inc.

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Feb 14, 2025

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: LDLR c.661G>A (p.Asp221Asn), also known as p.Asp200Asn, results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The frequency data for this variant in gnomAD is considered unreliable, as metrics indicate poor data quality at this position. c.661G>A has been reported in the literature in multiple heterozygous individuals and at-least one homozygous individual affected with Familial Hypercholesterolemia (example: Graesdal_2012, Sun_1997, Weiss_2000, Humphries_2006). These data indicate that the variant is very likely to be associated with disease. At least one publication reports the reduced degradation of radiolabeled LDL in cells derived from a patient harboring the variant, suggesting the variant impairs LDL-receptor function (Sun_1997). Furthermore, another missense variant affecting this amino acid (c.662A>G, p.Asp221Gly) has been classified as pathogenic by our laboratory, supporting the critical relevance of codon 221 to LDLR protein function. The following publications have been ascertained in the context of this evaluation (PMID: 22836070, 17142622, 9409298, 11196104). ClinVar contains an entry for this variant (Variation ID: 226331). Based on the evidence outlined above, the variant was classified as pathogenic. -

Oct 23, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 221 of the LDLR protein (p.Asp221Asn). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 1714262, 11196104, 17094996, 24075752, 25962062). Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this LDLR variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 363,995 individuals referred to our laboratory for LDLR testing. This variant is also known as c.661G>A, p.Asp200Asn. ClinVar contains an entry for this variant (Variation ID: 226331). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt LDLR protein function with a positive predictive value of 95%. This variant disrupts the p.Asp221 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 1301956, 19318025, 23375686, 25487149, 25647241). 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. -

Oct 12, 2018

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.661G>A (p.Asp221Asn) variant in the LDLR gene has been reported in multiple individuals with familial hypercholesterolemia (PMID: 9409298, 10090484, 11196104, 15199436, 15359125, 16250003, 17094996, 24075752, 25962062). The variant is not observed in gnomAD. The allelic change p.Asp221Tyr is an established pathogenic variant for FH. Functional studies demonstrated deleterious effect of the p.Asp221Asn variant. Multiple algorithms predicted this change to be deleterious. Therefore, the c.661G>A (p.Asp221Asn) variant in the LDLR gene is classified as pathogenic. -

not provided Pathogenic:2

Feb 20, 2023

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in multiple in individuals with familial hypercholesterolemia (FH) (PMID: 9409298 (1997), 9544745 (1998), 11196104 (2000), 34456200 (2021)), including one homozygous individual (PMID: 17142622 (2006)). It has also been reported in an individual with autosomal dominant hypercholesterolemia (ADH) (PMID: 16250003 (2005)), as well as in an otherwise healthy individual (PMID: 32719484 (2020)). A functional study found this variant was damaging to protein function (PMID: 9409298 (1997)). 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 damaging. Based on the available information, this variant is classified as pathogenic. -

May 25, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); Located in a region intolerant to change; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 22883975, 31447099, 16250003, 10090484, 11196104, 15359125, 19837725, 24075752, 35913489, 9544745, 33955087, 33740630, 32719484, 34037665) -

Cardiovascular phenotype Pathogenic:1

Oct 21, 2022

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.D221N variant (also known as c.661G>A), located in coding exon 4 of the LDLR gene, results from a G to A substitution at nucleotide position 661. The aspartic acid at codon 221 is replaced by asparagine, an amino acid with highly similar properties. This alteration has been reported in a number of individuals with familial hypercholesterolemia (Sun XM et al. Atherosclerosis, 1998 Jan;136:175-85; Ebhardt M et al. Hum. Mutat., 1999;13:257; Kim JH et al. Mol. Cells, 2004 Aug;18:63-70; Leren TP et al. Semin Vasc Med, 2004 Feb;4:75-85; Fouchier SW et al. Hum. Mutat., 2005 Dec;26:550-6). This alteration has also been reported as homozygous in a subject with tendom xanthomas and a total cholesterol of >500 mg/dL (Græsdal A et al. J Clin Lipidol Mar;6:331-9). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.88
BayesDel_addAF	Pathogenic	0.20	D
BayesDel_noAF	Uncertain	0.060
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.92	D;.;.;.
Eigen	Pathogenic	0.88
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.94	D;D;D;D
M_CAP	Pathogenic	0.77	D
MetaRNN	Pathogenic	0.99	D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.4	M;.;.;M
PrimateAI	Uncertain	0.53	T
PROVEAN	Pathogenic	-4.6	D;D;D;D
REVEL	Pathogenic	0.82
Sift	Uncertain	0.0010	D;D;D;D
Sift4G	Uncertain	0.0040	D;D;D;D
Polyphen		1.0	D;.;.;.
Vest4		0.82
MutPred		0.99		Loss of phosphorylation at S226 (P = 0.1334);Loss of phosphorylation at S226 (P = 0.1334);.;Loss of phosphorylation at S226 (P = 0.1334);
MVP		1.0
MPC		0.80
ClinPred		1.0	D
GERP RS		5.6
Varity_R		0.86
gMVP		0.99

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: rs875989906; hg19: chr19-11216243;