NM_000527.5:c.1474G>A

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PS4PS3PP1_StrongPM3PM2PP3PP4

This summary comes from the ClinGen Evidence Repository: The NM_000527.5 (LDLR):c.1474G>A (p.Asp492Asn) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying ACMG/AMP evidence codes PS3, PS4, PP1_Strong, PM2, PM3, PP3 and PP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (specification version 1.2) on 7 November 2023.The supporting evidence is as follows:PM2: PopMax MAF=0.00011 in East Asian population in gnomAD (gnomAD v2.1.1).PP3: REVEL=0.918.PS3: Level 1 assays, heterologous cells (CHO) used for Western blot and flow cytometry, showing diminished LDLR expression, 70% LDL binding and 49% uptake, reported in PMID 32015373 (Galicia-Garcia et al., 2020), Universidad del Pais Vasco, Spain.PS4, PP4: Variant meets PM2 and is identified in at least 43 unrelated index cases fulfilling clinical criteria for FH reported in ClinGen VCI and PubMed: 1 case reported from Cardiovascular Research group, Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal; 1 case from PathWest Laboratory Medicine WA, Australia; 5 cases from Service de Biochimie et de Biologie Moléculaire, Hospices Civils de Lyon, France; 2 cases from Mayo Clinic Atherosclerosis and Lipid Genomics Laboratory, USA; 2 cases from Research Lab of Molecular Genetics of Lipid Metabolism - Prof. M.Arca, Italy; 1 case from Robarts Research Institute, Canada; 6 cases from Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière, France; 11 cases from University Hospital Brno, Czech Republic and PMID 22698793 (Tichý et al., 2012). There are at least 14 index cases fulfilling FH clinical criteria in PMID 9763532, 11737238‚ 12436241‚ 17094996, 17539906‚ 19318025‚ 19446849‚ 20538126‚ 26748104, 28965616, 29353225, 30592178, 32331935, 32977124.PP1_Strong: Variants segregates with FH phenotype in at least 28 informative meiosis in 12 families from different labs (Cardiovascular Research group, Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal; University Hospital Brno, Czech Republic; PathWest Laboratory Medicine WA, Australia; Service de Biochimie et de Biologie Moléculaire, Hospices Civils de Lyon, France): 24 affected family members have the variant and 4 unaffected family members do not have the variant.PM3: 1 index case with HoFH phenotype (17 years female, LDL-C=12.44 mmol/L), also carries pathogenic LDLR p.Gly592Glu, confirmed in trans, reported from Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Czech Republic. LINK:https://erepo.genome.network/evrepo/ui/classification/CA023512/MONDO:0007750/013

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000062 ( 0 hom. )

Consequence

LDLR
NM_000527.5 missense

Scores

14
4
1

Clinical Significance

Pathogenic reviewed by expert panel P:21U:5O:1

Conservation

PhyloP100: 9.88
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PS3
For more information check the summary or visit ClinGen Evidence Repository.
PS4
For more information check the summary or visit ClinGen Evidence Repository.
PM2
For more information check the summary or visit ClinGen Evidence Repository.
PM3
For more information check the summary or visit ClinGen Evidence Repository.
PP1
For more information check the summary or visit ClinGen Evidence Repository.
PP3
For more information check the summary or visit ClinGen Evidence Repository.
PP4
For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LDLRNM_000527.5 linkc.1474G>A p.Asp492Asn missense_variant Exon 10 of 18 ENST00000558518.6 NP_000518.1 P01130-1A0A024R7D5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LDLRENST00000558518.6 linkc.1474G>A p.Asp492Asn missense_variant Exon 10 of 18 1 NM_000527.5 ENSP00000454071.1 P01130-1

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152198
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
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:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000239
AC:
6
AN:
251420
Hom.:
0
AF XY:
0.0000368
AC XY:
5
AN XY:
135896
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000352
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000616
AC:
9
AN:
1461738
Hom.:
0
Cov.:
35
AF XY:
0.00000963
AC XY:
7
AN XY:
727176
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000450
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152198
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.0000241
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:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000378
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.0000165
AC:
2
EpiCase
AF:
0.0000545
EpiControl
AF:
0.0000593

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:21Uncertain:5Other:1
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Hypercholesterolemia, familial, 1 Pathogenic:12Uncertain:4
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

- -

Mar 01, 2016
Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge
Significance: Uncertain significance
Review Status: flagged submission
Collection Method: research

0/184 non-FH alleles; 0/100 healthy control individuals -

Mar 10, 2020
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
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

- -

Dec 06, 2018
Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: research

- -

Jan 22, 2020
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: curation

The p.Asp492Asn (p.Asp471Asn) variant in LDLR has been reported in at least 30 individuals (including 13 Italian, 3 Chinese, 2 Norwegian, 2 Taiwanese, 1 Czech, and 1 Saudi Arabian individuals) with Familial Hypercholesterolemia, segregated with disease in up to 14 affected relatives from up to 7 families (PMID: 25647241, 26748104, 29172679, 11737238, 17094996, 23375686, 11005141, 25936317, 15199436, 17539906, 20538126, 9763532, 21310417, 12436241, 19446849; DOI: 10.2217/clp.14.6), and has been identified in 0.01087% (2/18394) of East Asian chromosomes and 0.003518% (4/113704) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs373646964). Please note that for diseases with clinical variability, or reduced penetrance, pathogenic variants may be present at a low frequency in the general population. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The phenotype of a homozygous individual with this variant is highly specific for Familial Hypercholesterolemia based on xanthomas and family history consistent with disease (DOI: 10.2217/clp.14.6). In summary, this variant meets criteria to be classified as pathogenic for Familial Hypercholesterolemia in an autosomal dominant manner based on multiple reports in individuals with Familial Hypercholesterolemia and cosegregation with disease. ACMG/AMP Criteria applied: PS4, PP1_Moderate, PP3, PP4 (Richards 2015). -

Mar 30, 2017
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

May 24, 2021
Laboratory of molecular diagnosis of dyslipidemias, Università egli studi di Napoli Federico II
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Class 5 - diminished LDLR recycling capacity. -

Mar 01, 2016
Laboratory of Genetics and Molecular Cardiology, University of São Paulo
Significance: Uncertain significance
Review Status: flagged submission
Collection Method: research

- -

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

subjects mutated among 2600 FH index cases screened = 10 , family members = 5 with unclear co-segregation / previously described in association with FH/Software predictions: Conflicting -

Mar 01, 2016
Fundacion Hipercolesterolemia Familiar
Significance: Uncertain significance
Review Status: flagged submission
Collection Method: research

- -

Apr 26, 2017
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This c.1474G>A (p.Asp492Asn) variant has been reported in a 42 year old male patient with familial hypercholesterolemia from a cohort of 30 patients [reported as D471N, FH Graz-1 in PMID 9763532]. This variant was also reported in a patient presenting with a total cholesterol level of 23 mmol/L and xanthomas [PMID 25936317]; this patient also carried a second allele (p.Gly592Glu), which is classified as pathogenic by our laboratory . This variant was further detected in a patient from a cohort of 2,078 patients from Italy [PMID 23375686]; this patient also carried a p.Cys698Trp variant, classified as a variant of unknown significance by our laboratory at this time. Additional variants affecting the same amino acid at position 492 (p.Asp492Gly and p.Asp492His) have been reported in patients with familial hypercholesterolemia [PMID 16250003, 10208479].This variant was reported in 2 heterozygous individuals in the ExAC database (http://exac.broadinstitute.org/variant/19-11224326-G-A). Asparagine at amino acid position 492 of the LDLR protein is highly conserved in mammals. While not validated for clinical use, the computer-based algorithms predict this p.Asp492Asn change to be deleterious. This variant is thus classified as likely pathogenic. -

Nov 07, 2019
Institute of Human Genetics, University of Leipzig Medical Center
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Criteria applied: PS3, PS4, PM2_SUP, PP3 -

-
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: research

- -

Jan 02, 2018
Robarts Research Institute, Western University
Significance: Uncertain significance
Review Status: flagged submission
Collection Method: clinical testing

- -

Nov 07, 2023
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel
Significance: Pathogenic
Review Status: reviewed by expert panel
Collection Method: curation

The NM_000527.5 (LDLR):c.1474G>A (p.Asp492Asn) variant is classified as Pathogenic for Familial Hypercholesterolemia by applying ACMG/AMP evidence codes PS3, PS4, PP1_Strong, PM2, PM3, PP3 and PP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (specification version 1.2) on 7 November 2023. The supporting evidence is as follows: PM2: PopMax MAF=0.00011 in East Asian population in gnomAD (gnomAD v2.1.1). PP3: REVEL=0.918. PS3: Level 1 assays, heterologous cells (CHO) used for Western blot and flow cytometry, showing diminished LDLR expression, 70% LDL binding and 49% uptake, reported in PMID 32015373 (Galicia-Garcia et al., 2020), Universidad del Pais Vasco, Spain. PS4, PP4: Variant meets PM2 and is identified in at least 43 unrelated index cases fulfilling clinical criteria for FH reported in ClinGen VCI and PubMed: 1 case reported from Cardiovascular Research group, Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal; 1 case from PathWest Laboratory Medicine WA, Australia; 5 cases from Service de Biochimie et de Biologie Moléculaire, Hospices Civils de Lyon, France; 2 cases from Mayo Clinic Atherosclerosis and Lipid Genomics Laboratory, USA; 2 cases from Research Lab of Molecular Genetics of Lipid Metabolism - Prof. M.Arca, Italy; 1 case from Robarts Research Institute, Canada; 6 cases from Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière, France; 11 cases from University Hospital Brno, Czech Republic and PMID 22698793 (Tichý et al., 2012). There are at least 14 index cases fulfilling FH clinical criteria in PMID 9763532, 11737238‚ 12436241‚ 17094996, 17539906‚ 19318025‚ 19446849‚ 20538126‚ 26748104, 28965616, 29353225, 30592178, 32331935, 32977124. PP1_Strong: Variants segregates with FH phenotype in at least 28 informative meiosis in 12 families from different labs (Cardiovascular Research group, Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal; University Hospital Brno, Czech Republic; PathWest Laboratory Medicine WA, Australia; Service de Biochimie et de Biologie Moléculaire, Hospices Civils de Lyon, France): 24 affected family members have the variant and 4 unaffected family members do not have the variant. PM3: 1 index case with HoFH phenotype (17 years female, LDL-C=12.44 mmol/L), also carries pathogenic LDLR p.Gly592Glu, confirmed in trans, reported from Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Czech Republic. -

Familial hypercholesterolemia Pathogenic:5
Jan 19, 2025
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 492 of the LDLR protein (p.Asp492Asn). This variant is present in population databases (rs373646964, gnomAD 0.01%). This missense change has been observed in individuals with familial hypercholesterolemia and myocardial infarction (PMID: 9763532, 10230472, 11005141, 20236128, 22698793, 23375686, 25487149, 25647241, 25936317, 27680772). It has also been observed to segregate with disease in related individuals. 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 Asp471Asn and Graz-1. ClinVar contains an entry for this variant (Variation ID: 161285). 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%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on LDLR function (PMID: 25647241). This variant disrupts the p.Asp492 amino acid residue in LDLR. Other variant(s) that disrupt this residue have been observed in individuals with LDLR-related conditions (PMID: 10208479, 16250003), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. -

May 06, 2021
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This c.1474G>A (p.Asp492Asn) variant has been reported in a 42 year old male patient with familial hypercholesterolemia from a cohort of 30 patients [reported as D471N, FH Graz-1 in PMID 9763532]. This variant was also reported in a patient presenting with a total cholesterol level of 23 mmol/L and xanthomas [PMID 25936317]; this patient also carried a second allele (p.Gly592Glu), which is classified as pathogenic by our laboratory . This variant was further detected in a patient from a cohort of 2,078 patients from Italy [PMID 23375686]; this patient also carried a p.Cys698Trp variant, classified as a variant of unknown significance by our laboratory at this time. Additional variants affecting the same amino acid at position 492 (p.Asp492Gly and p.Asp492His) have been reported in patients with familial hypercholesterolemia [PMID 16250003, 10208479].This variant was reported in 2 heterozygous individuals in the ExAC database (http://exac.broadinstitute.org/variant/19-11224326-G-A). Asparagine at amino acid position 492 of the LDLR protein is highly conserved in mammals. While not validated for clinical use, the computer-based algorithms predict this p.Asp492Asn change to be deleterious. This variant is thus classified as likely pathogenic. -

Jun 05, 2017
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Variant summary: The LDLR c.1474G>A (p.Asp492Asn) variant involves the alteration of a conserved nucleotide. 4/5 in silico tools predict a damaging outcome for this variant. This variant was found in 2/121480 control chromosomes at a frequency of 0.0000165, which does not exceed the estimated maximal expected allele frequency of a pathogenic LDLR variant (0.0012508). This variant has been reported in multiple affected FH patients including heterozygous patients and compound heterozygous patients (Mak_1998, Chiou_2010, Bertolini_2013, Blaha_2015). Variant was shown to segregate with disease in at least one of the reported families (Blaha_2015). Variants involving nearby nucleotides such as c.1474G>C, c.1474delG, c.1475A>G, etc, have been reported in affected individuals suggesting variant of interest is located in a mutiaotn hotspot. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely pathogenic. Taken together, this variant is classified as pathogenic. -

Jul 18, 2024
Laboratory of Molecular Genetics, National Medical Research Center for Therapy and Preventive Medicine
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: research

Based on the ACMG/AMP 2015 guidelines (Richards 2015), p.Asp492Asn variant has the following pathogenicity criteria: PM1- located in the EGF-precursor homology domain: YWTD repeat (Galicia-Garcia 2020, Jeon 2001); PM2 - detected in control samples of gnomAD v4.1.0 with a frequency of 0.0006196%; PM5 - missense variant at the same codon as a variant classified as pathogenic (c.1474G>C, p.Asp492His (ClinVar ID 251864)) or likely pathogenic (c.1475A>G, p.Asp492Gly (ClinVar ID 251865)) and predicts a different amino acid change; PP1_Strong - segregated with FH in 6 relativities in 1 family (4 - 1st degree relatives and 2 - 2nd degree relatives) (Faiz 2014); PP3; PP4-registered in patients with FH. According to the ClinGen guidelines for LDLR variant classification (Chora 2022), PS4 - variant has been found in ≥10 unrelated FH cases, including 1 FH case in Russia (Meshkov 2021); PM2 - has a PopMax MAF ≤ 0.0002 (0.02%) in gnomAD (0.0006196% v4.1.0 gnomAD); PM5 - missense variant at the same codon as a variant classified as pathogenic (c.1474G>C, p.Asp492His (ClinVar ID 251864)) and predicts a different amino acid change; PP1_Strong -segregates with phenotype in 6 informative meioses in 1 family (Faiz 2014); PP3 - REVEL score 0.918 (Liu 2011, Liu 2020); PP4 - identified in 1 proband with FH based on DLCN-criteria (11 points) (data from the Laboratory of Molecular Genetics, Moscow, Russia (Meshkov 2021)). Based on a combination of criteria, this variant is pathogenic. -

Feb 01, 2023
Color Diagnostics, LLC DBA Color Health
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This missense variant replaces aspartic acid with asparagine at codon 492 in the third LDLR type B repeat of the EGF precursor homology domain of the LDLR protein. This variant is also known as p.Asp471Asn in the mature protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). A functional study has shown that this variant results in the partially reduced levels of LDLR protein expression at the cell surface, reduced LDL binding, and a defect in LDLR protein recycling (PMID: 35568682). Another study has suggested no to little impact of this variant on LDL uptake (PMID: 25647241). This variant has been observed in over twenty heterozygous individuals affected with familial hypercholesterolemia (PMID: 9763532, 11737238, 12436241, 15199436, 15823288, 17539906, 19318025, 19446849, 20538126, 21310417, 22698793, 25936317, 35249492; Color data) and in two biallelic individuals with severe phenotype (PMID: 25936317, 30592178). This variant has been shown segregate with disease in a family study (PMID: 25936317). This variant has been identified in 6/251420 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different missense variants occurring at the same position, p.Asp492His and p.Asp492Gly, are known to be disease-causing (ClinVar variation ID: 251864, 251865). Based on the available evidence, this variant is classified as Pathogenic. -

not provided Pathogenic:3Other:1
Nov 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jul 21, 2022
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies demonstrate reduced protein expression, receptor binding, and LDL uptake (Galicia-Garcia et al., 2020); Not observed at significant frequency in large population cohorts (gnomAD); Also known as p.D471N and FH-Graz 1; This variant is associated with the following publications: (PMID: 25647241, 27535533, 10230472, 23375686, 25487149, 25637381, 29292049, 27680772, 19446849, 21310417, 22698793, 29172679, 17539906, 26875521, 28965616, 29353225, 25936317, 26748104, 30592178, 31447099, 11005141, 12436241, 15199436, 11737238, 20538126, 20236128, 17094996, 30526649, 32977124, 32041611, 32331935, 33740630, 34037665, 32015373, 26582918, 9763532) -

-
Dept. of Genetics and Pharmacogenomics, Merck Research Labs
Significance: not provided
Review Status: no classification provided
Collection Method: in vitro

- -

Feb 08, 2024
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The LDLR c.1474G>A; p.Asp492Asn variant (rs373646964) is reported in the literature in the heterozygous or compound heterozygous states in numerous individuals affected with familial hypercholesterolemia (Benedek 2021, Bertolini 2013, Blaha 2015, Huang 2022, Mak 1998, Pirillo 2017, Tada 2020, Wang 2020). This variant is also reported in ClinVar (Variation ID: 161285). This variant is found in the general population with an overall allele frequency of 0.002% (6/251,420 alleles) in the Genome Aggregation Database (v2.1.1). Additionally, other variants at this codon (c.1475A>G, p.Asp492Gly; c.1474G>C, p.Asp492His) have been reported in individuals with familial hypercholesterolemia and are considered to be disease causing (Fouchier 2005, Sturm 2021). Computational analyses predict that this variant is deleterious (REVEL: 0.918). In vitro functional analyses demonstrate the variant protein has significantly reduced LDLR expression, binding and internalization compared to WT (Graca 2022). However, additional in vitro functional analyses demonstrate non-disruptive LDL uptake (Thormaehlen 2015). Based on available information, this variant is considered to be pathogenic. References: Benedek P et al. Founder effects facilitate the use of a genotyping-based approach to molecular diagnosis in Swedish patients with familial hypercholesterolaemia. J Intern Med. 2021 Aug;290(2):404-415. PMID: 33955087. Bertolini S et al. Spectrum of mutations and phenotypic expression in patients with autosomal dominant hypercholesterolemia identified in Italy. Atherosclerosis. 2013 Apr;227(2):342-8. PMID: 23375686. Blaha M et al. Pregnancy in homozygous familial hypercholesterolemia--Importance of LDL-apheresis. Atheroscler Suppl. 2015 May;18:134-9. PMID: 25936317. Fouchier SW et al. Update of the molecular basis of familial hypercholesterolemia in The Netherlands. Hum Mutat. 2005 Dec;26(6):550-6. PMID: 16250003. Graca R et al. Functional profiling of LDLR variants: Important evidence for variant classification: Functional profiling of LDLR variants. J Clin Lipidol. 2022 Jul-Aug;16(4):516-524. PMID: 35568682. Huang CC et al. Genetic Analysis in a Taiwanese Cohort of 750 Index Patients with Clinically Diagnosed Familial Hypercholesterolemia. J Atheroscler Thromb. 2022 May 1;29(5):639-653. PMID: 33994402. Mak YT et al. Mutations in the low-density lipoprotein receptor gene in Chinese familial hypercholesterolemia patients. Arterioscler Thromb Vasc Biol. 1998 Oct;18(10):1600-5. PMID: 9763532. Pirillo A et al. Spectrum of mutations in Italian patients with familial hypercholesterolemia: New results from the LIPIGEN study. Atheroscler Suppl. 2017 Oct;29:17-24. PMID: 28965616. Sturm AC et al. Limited-Variant Screening vs Comprehensive Genetic Testing for Familial Hypercholesterolemia Diagnosis. JAMA Cardiol. 2021 Aug 1;6(8):902-909. PMID: 34037665. Tada H et al. A catalog of the pathogenic mutations of LDL receptor gene in Japanese familial hypercholesterolemia. J Clin Lipidol. 2020 May-Jun;14(3):346-351.e9. PMID: 32331935. Thormaehlen AS et al. Systematic cell-based phenotyping of missense alleles empowers rare variant association studies: a case for LDLR and myocardial infarction. PLoS Genet. 2015 Feb 3;11(2):e1004855. PMID: 25647241. Wang H et al. Targeted Genetic Analysis in a Chinese Cohort of 208 Patients Related to Familial Hypercholesterolemia. J Atheroscler Thromb. 2020 Dec 1;27(12):1288-1298. PMID: 32759540. -

Cardiovascular phenotype Pathogenic:1
Mar 08, 2024
Ambry Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The p.D492N pathogenic mutation (also known as c.1474G>A), located in coding exon 10 of the LDLR gene, results from a G to A substitution at nucleotide position 1474. The aspartic acid at codon 492 is replaced by asparagine, an amino acid with highly similar properties. This alteration has been reported in the homozygous state in a case with familial hypercholesterolemia (FH), corneal arcus, xanthelasmata, and tendon xanthomas; six heterozygous family members also had elevated cholesterol levels and other clinical symptoms (Faiz F et al. Clin Lipidol., 2014 April; 9:163-170). In addition, compound heterozygotes with this alteration demonstrated clinical symptoms of FH (Blaha M et al. Atheroscler Suppl, 2015 May;18:134-9; Bertolini S et al. Atherosclerosis, 2013 Apr;227:342-8). This alteration, historically known as D471N, has been reported in several FH and myocardial infarction (MI) cohorts (Mak YT et al. Arterioscler. Thromb. Vasc. Biol., 1998 Oct;18:1600-5; Chiou KR et al. Am. J. Cardiol., 2010 Jun;105:1752-8; Tichý L et al. Atherosclerosis, 2012 Aug;223:401-8; Do R et al. Nature, 2015 Feb;518:102-6). The variant was reported in an individual with early-onset MI and CAD with reportedly normal LDL level; however, details were limited. The associated functional study failed to show negative effects for the variant in vitro, but the physiological relevance of the assay results are unclear (Thormaehlen AS et al. PLoS Genet., 2015 Feb;11:e1004855). Another in vitro functional study reported this variant to result in reduced protein expression, activity, and recycling compared to wild type (Galicia-Garcia U et al. Sci Rep. 2020 02;10(1):1727). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Hypercholesterolemia Uncertain:1
Jun 01, 2014
CSER _CC_NCGL, University of Washington
Significance: Uncertain significance
Review Status: flagged submission
Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.84
BayesDel_addAF
Uncertain
0.14
D
BayesDel_noAF
Pathogenic
0.19
CADD
Pathogenic
32
DANN
Pathogenic
1.0
DEOGEN2
Pathogenic
0.92
D;.;.;.;.;.
Eigen
Pathogenic
0.82
Eigen_PC
Pathogenic
0.73
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Pathogenic
1.0
D;D;D;D;D;D
M_CAP
Pathogenic
0.91
D
MetaRNN
Pathogenic
0.97
D;D;D;D;D;D
MetaSVM
Pathogenic
1.0
D
MutationAssessor
Pathogenic
3.0
M;.;.;.;.;M
PrimateAI
Uncertain
0.57
T
PROVEAN
Pathogenic
-4.7
D;D;D;D;D;D
REVEL
Pathogenic
0.92
Sift
Uncertain
0.024
D;D;D;D;D;D
Sift4G
Uncertain
0.024
D;D;D;D;D;D
Polyphen
1.0
D;.;.;.;.;.
Vest4
0.89
MVP
1.0
MPC
0.80
ClinPred
0.94
D
GERP RS
4.7
Varity_R
0.86
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

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

Other links and lift over

dbSNP: rs373646964; hg19: chr19-11224326; COSMIC: COSV52946004; COSMIC: COSV52946004; API