rs749038326

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong

The NM_000527.5(LDLR):c.268G>A(p.Asp90Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,844 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 Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D90A) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000020 ( 0 hom. )

Consequence

LDLR
NM_000527.5 missense

Scores

Clinical Significance

Pathogenic reviewed by expert panel P:20B:1

Conservation

PhyloP100: 9.95

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PM1

In a hotspot region, there are 10 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 9 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 chr19-11102742-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 440555.Status of the report is reviewed_by_expert_panel, 3 stars.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.971

PP5

Variant 19-11102741-G-A is Pathogenic according to our data. Variant chr19-11102741-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 251105.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr19-11102741-G-A is described in Lovd as [Pathogenic]. Variant chr19-11102741-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LDLR	NM_000527.5 linkuse as main transcript	c.268G>A	p.Asp90Asn	missense_variant	3/18	ENST00000558518.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LDLR	ENST00000558518.6 linkuse as main transcript	c.268G>A	p.Asp90Asn	missense_variant	3/18	1	NM_000527.5	P3	P01130-1

Frequencies

GnomAD3 genomes

AF:

0.0000197

AC:

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000557

AC:

AN:

251486

Hom.:

AF XY:

0.0000441

AC XY:

AN XY:

135920

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000707

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000198

AC:

AN:

1461702

Hom.:

Cov.:

AF XY:

0.0000193

AC XY:

AN XY:

727160

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000277

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000135

Gnomad4 OTH exome

AF:

0.0000331

GnomAD4 genome

AF:

0.0000197

AC:

AN:

152142

Hom.:

Cov.:

AF XY:

0.0000269

AC XY:

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000191

Hom.:

Bravo

AF:

0.00000756

ExAC

AF:

0.0000494

AC:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:20Benign:1

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Hypercholesterolemia, familial, 1

Pathogenic:10Benign:1

Likely benign, 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 , family members = 2 with co-segregation / other mutations at same codon / Software predictions: Damaging -
Pathogenic, criteria provided, single submitter	research	Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia	Jan 15, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jan 06, 2024	This missense variant replaces aspartic acid with asparagine at codon 90 in the second LDLR type A of the ligand binding domain of the LDLR protein. This variant is also known as p.Asp69Asn 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). A functional study has shown that the mutant protein is trapped in the endoplasmic reticulum and shows weak cell surface expression (PMID: 12837857). Cells from an individual compound heterozygous for this variant and p.Cys222* showed no detectable LDLR activity (PMID: 16343504). This variant has been reported in over thirty individuals of varying ethnicities affected with familial hypercholesterolemia (PMID: 9259195, 9763532, 12436241, 12837857, 15823276, 16250003, 16343504, 21376320, 23375686, 25962062, 27206935, 31345425) and is thought to be one of the most common pathogenic mutation in the Chinese population (PMID: 27206935, 30592178, 31686828). This variant has been reported to segregate with disease in one family (PMID: 12837857). This variant has been identified in 17/282878 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different missense variants occurring at this codon, p.Asp90Gly and p.Asp90AGlu, are known to cause disease (ClinVar variation ID: 226313, 251107), suggesting that aspartic acid at this position is important for LDLR protein function. Based on the available evidence, this variant is classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	literature only	LDLR-LOVD, British Heart Foundation	Mar 25, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille	Mar 30, 2017	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	Aug 28, 2022	The NM_000527.5(LDLR):c.268G>A (p.Asp90Asn) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying evidence codes PM5_Strong, PM2, PP1_Moderate, PS3_Moderate, PS4_Moderate and 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: PM5_strong - there are 4 other missense variants is the same codon: - NM_000527.5(LDLR):c.268G>T (p.Asp90Tyr) - classified as Likely pathogenic by the FH VCEP, with these guidelines - NM_000527.5(LDLR):c.269A>C (p.Asp90Ala) - Likely pathogenic by these guidelines - NM_000527.5(LDLR):c.269A>G (p.Asp90Gly) - Pathogenic by these guidelines - NM_000527.5(LDLR):c.270T>A (p.Asp90Glu) - Pathogenic by these guidelines --- There are 2 variants classified as Pathogenic, so PM5_Strong is met. PP1_moderate - Variant segregates with phenotype in 4 informative meiosis from different labs: - 1 unaffected family member does not have the variant, from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation); - 3 informative meiosis from 1 family from PMID 12837857 (Chang et al. 2003): 1 relative has the variant and phenotype (III:1), plus 2 relatives do not have the variant and do not have the phenotype (II:1 and III:2) 4 informative meiosis, so PP1_Moderate is met. PM2 - PopMax MAF = 0.0008019 (0.08019%) in East Asian (gnomAD v2.1.1), but this is a founder variant in East Asian populations, so PM2 can be met in this instance. PS3_moderate - Level 2 FS: Chang et al., 2003 (PMID:12837857): Heterologous cells (COS-7), FACS assays - results: 55% LDLR cell surface and uptake. Binding is not studied, so not all cycle is studied (level 2 and not level 1) ---- functional study is consistent with damaging effect, activity is below 70% of wild-type, so PS3_Moderate is met. PS4_moderate - variant meets PM2 and was identified in: - 1 index case who fulfills Simon Broome criteria of possible FH from Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation), Czech Republic; - 3 unrelated index cases, all with Dutch lipid clinic network >=6, from Robarts Research Institute, Canada; - at least 1 index case with DLCN score of definite FH from U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille (SCV000583645.1 in ClinVar), France; - 1 index case who fulfills SB criteria of at least possible FH from PMID 9259195 (Day et al., 1997), UK; - 1 index case who fulfills SB criteria of at least possible FH from PMID 25962062 (Han et al., 2015), Korea; - 2 unrelated index cases who fulfill SB criteria of possible FH (TC>8mmol/L, plus CAD) from PMID 12837857 (Chang et al., 2003), Taiwan, China; 9 cases, so PS4_Moderate is met. PP4 - variant meets PM2 and was identified in 9 unrelated index cases from different labs (see PS4 for details), so PP4 is met. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Robarts Research Institute, Western University	-	- -
Pathogenic, no assertion criteria provided	research	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jun 28, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Oct 19, 2020	Based on the classification scheme VCGS_Germline_v1.3.2, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with familial hypercholesterolemia. (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance (Gene Reviews). (I) 0200 - Variant is predicted to result in a missense amino acid change from aspartic acid to asparagine (exon 3). (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (17 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a minor amino acid change. (SP) 0600 - Variant is located in the annotated calcium binding site of low-density lipoprotein receptor domain class A (NCBI). (I) 0701 - Other missense variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Four different variants in the same codon resulting in changes to tyrosine, alanine, glutamic acid and glycine have all been shown to cause familial hypercholesterolemia (ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. The variant has been previously reported in patients with familial hypercholesterolemia (ClinVar, PMID: 30649024). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Functional studies using COS7 cells show that this variant causes retention in the endoplasmic reticulum and reduction in LDLR activity (PMID: 12837857). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Likely pathogenic, criteria provided, single submitter	curation;literature only	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	Mar 01, 2016	- -

not provided

Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Feb 06, 2024	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Feb 17, 2023	Described as one of the most frequent variants associated with FH in the Han Chinese population (Chiou and Charng, 2016); Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate reduced receptor protein on cell surface and reduced LDL binding and internalization (Chang et al., 2003); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(Asp69Asn); This variant is associated with the following publications: (PMID: 22390909, 9259195, 24956927, 28235710, 34037665, 12837857, 32977124, 32041611, 33391346, 33994402, 32759540, 23375686, 27206935) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Dec 29, 2021	PM5, PS3, PS4 -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -

Familial hypercholesterolemia

Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Sep 01, 2023	This missense variant replaces aspartic acid with asparagine at codon 90 in the second LDLR type A of the ligand binding domain of the LDLR protein. This variant is also known as p.Asp69Asn 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). A functional study has shown that the mutant protein is trapped in the endoplasmic reticulum and shows weak cell surface expression (PMID: 12837857). Cells from an individual compound heterozygous for this variant and p.Cys222* showed no detectable LDLR activity (PMID: 16343504). This variant has been reported in over thirty individuals of varying ethnicities affected with familial hypercholesterolemia (PMID: 9259195, 9763532, 12436241, 12837857, 15823276, 16250003, 16343504, 21376320, 23375686, 25962062, 27206935, 31345425) and is thought to be one of the most common pathogenic mutation in the Chinese population (PMID: 27206935, 30592178, 31686828). This variant has been reported to segregate with disease in one family (PMID: 12837857). This variant has been identified in 17/282878 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different missense variants occurring at this codon, p.Asp90Gly and p.Asp90AGlu, are known to cause disease (ClinVar variation ID: 226313, 251107), suggesting that aspartic acid at this position is important for LDLR protein function. Based on the available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 24, 2024	This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 90 of the LDLR protein (p.Asp90Asn). This variant is present in population databases (rs749038326, gnomAD 0.08%). This missense change has been observed in individuals with familial hypercholesterolemia (PMID: 9259195, 9763532, 12436241, 12837857, 15823276, 16343504, 21376320, 22390909, 23375686, 25962062, 27206935, 27765764). This variant is also known as p.Asp69Asn. ClinVar contains an entry for this variant (Variation ID: 251105). 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: 12837857). This variant disrupts the p.Asp90 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 1301956, 8347689, 19026292). 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Sep 08, 2021	Variant summary: LDLR c.268G>A (p.Asp90Asn) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.6e-05 in 251486 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in LDLR causing Familial Hypercholesterolemia (5.6e-05 vs 0.0013), allowing no conclusion about variant significance. c.268G>A has been reported in the literature in multiple individuals affected with Familial Hypercholesterolemia (Mak_1998, Chiou_2016, Fouchier_2005, Chiou_2010). Functional studies have shown the variant to impact LDLR subcellular localization and reduces LDLR activity (Chang_2003). Other variants have been reported in association with Hypercholesterolemia (D90A, D90E, D90G, D90Y). Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Seven submitters classified as likely pathogenic/pathogenic while one classified as likely benign. Based on the evidence outlined above, the variant was classified as pathogenic. -

Homozygous familial hypercholesterolemia

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Apr 08, 2019

The p.Asp90Asn variant in LDLR has been identified in at least 15 individuals with familial hypercholesterolemia (FH): In 12 individuals in the heterozygous state (Day 1997, Mak 1998, Amsellem 2002, Chang 2003, Sozen 2005, Chiou 2011, Bertolini 2013, Norsworthy 2014, Han 2015, Wang 2016, Hsiung 2018) and in 3 invididuals in the compound heterozygous state who had significantly higher serum LDL levels (Bertonlini 2013, Hsiung 2018). It has also been reported by other clinical laboratories in ClinVar (Variation ID 251105) and has been identified in 0.08% (16/19952) of East Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). An in vitro functional study (Chang 2003) and computational and conservation analysis support an impact on protein function. Additionally, several other variants involving this codon (p.Asp90Tyr, p.Asp90Ala, p.Asp90Gly, and p.Asp90Glu) have been identified in individuals with FH (Stenson 2017), suggesting that changes as this position are not tolerated. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant FH based upon case observations and functional and computational evidence. ACMG/AMP criteria applied: PM3_Strong, PS4_Moderate, PP3, PS3_Supporting. -

Cardiovascular phenotype

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 04, 2023

The c.268G>A (p.D90N) alteration is located in exon 3 (coding exon 3) of the LDLR gene. This alteration results from a G to A substitution at nucleotide position 268, causing the aspartic acid (D) at amino acid position 90 to be replaced by an asparagine (N). Based on data from gnomAD, the A allele has an overall frequency of 0.006% (17/282878) total alleles studied. The highest observed frequency was 0.08% (16/19952) of East Asian alleles. This alteration, also known as p.D69N, has been reported in multiple individuals with familial hypercholesterolemia (FH) and in FH cohorts from a variety of ethnic backgrounds (Day, 1997; Mak, 1998; Khoo, 2000; Chang, 2003; Fouchier, 2005; Norsworthy, 2014). Other amino acid substitutions at this position have also been reported in individuals with FH, including D90A (Kolansky, 2008), D90E (Marduel, 2010), D90G (Hobbs, 1992), and D90Y (Rubinsztein, 1993). This amino acid position is highly conserved in available vertebrate species. Based on internal structural analysis, this alteration occurs in a known motif in a region of known function with an effect that matches known phenotype (Kurniawan, 2000). The results of functional studies demonstrated that protein product is retained in the endoplasmic reticulum and enzyme activity is reduced (Chang, 2003). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.52

BayesDel_addAF

Benign

-0.081

BayesDel_noAF

Uncertain

0.020

Cadd

Pathogenic

Dann

Uncertain

1.0

DEOGEN2

Pathogenic

0.89

D;.;.;.;.

Eigen

Uncertain

0.55

Eigen_PC

Uncertain

0.49

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Pathogenic

0.98

D;D;D;D;D

M_CAP

Pathogenic

0.71

MetaRNN

Pathogenic

0.97

D;D;D;D;D

MetaSVM

Pathogenic

1.1

MutationAssessor

Uncertain

2.2

M;.;M;M;M

MutationTaster

Benign

1.0

D;D;D;D;D;D;D

PrimateAI

Benign

0.47

PROVEAN

Pathogenic

-4.6

D;D;N;D;D

Sift

Pathogenic

0.0

D;D;T;D;D

Sift4G

Uncertain

0.0050

D;D;T;D;D

Polyphen

1.0

D;.;.;.;.

Vest4

0.73

MutPred

0.92

Gain of MoRF binding (P = 0.0707);Gain of MoRF binding (P = 0.0707);Gain of MoRF binding (P = 0.0707);Gain of MoRF binding (P = 0.0707);Gain of MoRF binding (P = 0.0707);

MVP

1.0

MPC

0.80

ClinPred

0.48

GERP RS

5.7

Varity_R

0.95

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over