U.S. flag

An official website of the United States government

NM_000527.5(LDLR):c.682G>A (p.Glu228Lys) AND Hypercholesterolemia, familial, 1

Germline classification:
Pathogenic (18 submissions)
Last evaluated:
Apr 30, 2022
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000003878.36

Allele description [Variation Report for NM_000527.5(LDLR):c.682G>A (p.Glu228Lys)]

NM_000527.5(LDLR):c.682G>A (p.Glu228Lys)

Gene:
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_000527.5(LDLR):c.682G>A (p.Glu228Lys)
Other names:
E207K; FH Mexico; FH French Canadian 3; FH Canadian-3; FH Modena; FH French Canadian-3; FH Mexico 3; NP_000518.1:p.E228K; NM_000527.5(LDLR):c.682G>A
HGVS:
  • NC_000019.10:g.11105588G>A
  • NG_009060.1:g.21208G>A
  • NM_000527.5:c.682G>AMANE SELECT
  • NM_001195798.2:c.682G>A
  • NM_001195799.2:c.559G>A
  • NM_001195800.2:c.314-1804G>A
  • NM_001195803.2:c.314-977G>A
  • NP_000518.1:p.Glu228Lys
  • NP_000518.1:p.Glu228Lys
  • NP_001182727.1:p.Glu228Lys
  • NP_001182728.1:p.Glu187Lys
  • LRG_274t1:c.682G>A
  • LRG_274:g.21208G>A
  • LRG_274p1:p.Glu228Lys
  • NC_000019.9:g.11216264G>A
  • NM_000527.4:c.682G>A
  • P01130:p.Glu228Lys
  • c.682G>A
Protein change:
E187K; GLU207LYS
Links:
LDLR-LOVD, British Heart Foundation: LDLR_000105; UniProtKB: P01130#VAR_005341; OMIM: 606945.0007
Molecular consequence:
  • NM_001195800.2:c.314-1804G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195803.2:c.314-977G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000527.5:c.682G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195798.2:c.682G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195799.2:c.559G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
9

Condition(s)

Name:
Hypercholesterolemia, familial, 1
Synonyms:
LDL RECEPTOR DISORDER; Hyperlipoproteinemia Type IIa; HYPER-LOW-DENSITY-LIPOPROTEINEMIA; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007750; MedGen: C0745103; Orphanet: 391665; OMIM: 143890

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000024043OMIM
no assertion criteria provided
Pathogenic
(Apr 1, 1990)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000268581Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital
no assertion criteria provided
Pathogenic
(Jul 20, 2012)
germlineclinical testing

SCV000294905LDLR-LOVD, British Heart Foundation
criteria provided, single submitter

(ACGS Guidelines, 2013)
Likely pathogenic
(Mar 25, 2016)
germlineliterature only

PubMed (10)
[See all records that cite these PMIDs]

Citation Link,

SCV000322911Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 1, 2016)
germlineresearch

PubMed (3)
[See all records that cite these PMIDs]

SCV000484738Robarts Research Institute, Western University
criteria provided, single submitter

(Wang et al. (Arterioscler Thromb Vasc Biol. 2016))
Likely pathogenicgermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000503221Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 16, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000540754Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Nov 5, 2016)
unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV000583724U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 30, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000588511Laboratory of Genetics and Molecular Cardiology, University of São Paulo - HipercolBrasil
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 1, 2016)
germlineresearch

PubMed (3)
[See all records that cite these PMIDs]

SCV000606201Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum
no assertion criteria provided
Pathogenicgermlineresearch

SCV000607494Fundacion Hipercolesterolemia Familiar - SAFEHEART
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 1, 2016)
germlineresearch

PubMed (3)
[See all records that cite these PMIDs]

SCV000733815Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus
no assertion criteria provided
Pathogenicgermlineclinical testing

SCV000743851Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus
criteria provided, single submitter

(ACGS Guidelines, 2013)
Pathogenic
(Jul 28, 2017)
germlineclinical testing

Citation Link,

SCV000748039Iberoamerican FH Network
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 1, 2016)
germlineresearch

PubMed (3)
[See all records that cite these PMIDs]

SCV000894170Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 31, 2018)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001432572Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jan 20, 2019)
germlineresearch

PubMed (2)
[See all records that cite these PMIDs]

SCV001467728Rajaie Cardiovascular, Medical and Research Center, Iran University of Medical Sciences
no assertion criteria provided
Pathogenicsomaticresearch

SCV002506410ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel
reviewed by expert panel

(ClinGen FH ACMG Specifications v1-2)
Pathogenic
(Apr 30, 2022)
germlinecuration

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes348not provided2611not providedclinical testing, research, literature only
not providedgermlineunknownnot providednot providednot providednot providednot providedresearch, curation
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedsomaticyes1not providednot providednot providednot providedresearch
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
Caucasianunknownyes11not provided3964not providedclinical testing

Citations

PubMed

Deletion in the first cysteine-rich repeat of low density lipoprotein receptor impairs its transport but not lipoprotein binding in fibroblasts from a subject with familial hypercholesterolemia.

Leitersdorf E, Hobbs HH, Fourie AM, Jacobs M, van der Westhuyzen DR, Coetzee GA.

Proc Natl Acad Sci U S A. 1988 Nov;85(21):7912-6.

PubMed [citation]
PMID:
3263645
PMCID:
PMC282319

Clinical expression of familial hypercholesterolemia in clusters of mutations of the LDL receptor gene that cause a receptor-defective or receptor-negative phenotype.

Bertolini S, Cantafora A, Averna M, Cortese C, Motti C, Martini S, Pes G, Postiglione A, Stefanutti C, Blotta I, Pisciotta L, Rolleri M, Langheim S, Ghisellini M, Rabbone I, Calandra S.

Arterioscler Thromb Vasc Biol. 2000 Sep;20(9):E41-52.

PubMed [citation]
PMID:
10978268
See all PubMed Citations (16)
PMC

Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424

PMC [article]
PMCID:
PMC4544753
PMID:
25741868
DOI:
10.1038/gim.2015.30

Details of each submission

From OMIM, SCV000024043.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Codon 207 (GAG) is changed to AAG (Leitersdorf and Hobbs, 1990). The same mutation was found in French Canadians with FHCL1 (143890) (Leitersdorf et al., 1990).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital, SCV000268581.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences

From LDLR-LOVD, British Heart Foundation, SCV000294905.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedliterature only PubMed (10)
2not provided1not providednot providedliterature only PubMed (10)
3not provided1not providednot providedliterature only PubMed (10)
4not provided1not providednot providedliterature only PubMed (10)
5not provided1not providednot providedliterature only PubMed (10)
6not provided1not providednot providedliterature only PubMed (10)
7not provided1not providednot providedliterature only PubMed (10)
8not provided1not providednot providedliterature only PubMed (10)
9not provided1not providednot providedliterature only PubMed (10)
10not provided1not providednot providedliterature only PubMed (10)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided
2germlineyes1not providednot provided1not providednot providednot provided
3germlineyes1not providednot provided1not providednot providednot provided
4germlineyes1not providednot provided1not providednot providednot provided
5germlineyes1not providednot provided1not providednot providednot provided
6germlineyes1not providednot provided1not providednot providednot provided
7germlineyes1not providednot provided1not providednot providednot provided
8germlineyes1not providednot provided1not providednot providednot provided
9germlineyes1not providednot provided1not providednot providednot provided
10germlineyes1not providednot provided1not providednot providednot provided

From Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge, SCV000322911.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (3)
2not providednot providednot providednot providedresearch PubMed (3)

Description

"Homozygous / Heterozygous patients' fibroblast, 125I-LDL assays"

Description

0/190 non-FH alleles; 0/100 Chinese normolipidemic individuals; 0/100 healthy control individuals

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided
2germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Robarts Research Institute, Western University, SCV000484738.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix, SCV000503221.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided9not providednot providedclinical testing PubMed (1)

Description

subjects mutated among 2600 FH index cases screened = 9 , family members = 3 with co-segregation / FH-Canada-3, < 2% LDLR Activity / Software predictions: Damaging

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes2600not providednot provided9not providednot providednot provided

From Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, SCV000540754.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Caucasian1not providednot providedclinical testing PubMed (2)

Description

Disrupt SDE motif. SDE bind structural Ca2+.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes3964Whole bloodnot provided1not provided1not provided

From U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille, SCV000583724.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided12not providednot providedclinical testing PubMed (1)

Description

Dutch Lipid Clinic Scoring : Definite FH

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided12not provided8not provided

From Laboratory of Genetics and Molecular Cardiology, University of São Paulo - HipercolBrasil, SCV000588511.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (3)
2not providednot providednot providednot providedresearch PubMed (3)

Description

"Assay description:Hmz / Htz patients' fibroblast, 125I-LDL assays"
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided
2germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum, SCV000606201.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Fundacion Hipercolesterolemia Familiar - SAFEHEART, SCV000607494.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (3)
2not providednot providednot providednot providedresearch PubMed (3)

Description

"Hmz / Htz patients' fibroblast, 125I-LDL assays"
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided
2germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000733815.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV000743851.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Iberoamerican FH Network, SCV000748039.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (3)
2not providednot providednot providednot providedresearch PubMed (3)

Description

"Assay Description:Hmz / Htz patients' fibroblast, 125I-LDL assays"
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided
2germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV000894170.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia, SCV001432572.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

From Rajaie Cardiovascular, Medical and Research Center, Iran University of Medical Sciences, SCV001467728.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedresearchnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1somaticyesnot providednot providednot provided1not providednot providednot provided

From ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel, SCV002506410.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_000527.5(LDLR):c.682G>A (p.Glu228Lys) variant is classified as pathogenic for Familial Hypercholesterolemia by applying evidence code PS3, PS4, PM1, PM2, PP1_Strong, PP3 and PP4 as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: PM2 - PopMax MAF = 0.0001105 (0.01%) in East Asian exomes (gnomAD v2.1.1). PP3 - REVEL = 0.972. It is above 0.75. PM1 - Variant meets PM2 and is missense located in exon 4 . PS3 - Three studies contribute to PS3 attribution. One (PMID: 10978268) report a level 3 assay performed on heterozygous patient's fibroblasts with radiolabeled LDL consistent with damaging effect of the variant (50% LDLR activity). The second reports a level 2 assay perfomed on homozygous patient's fibroblasts with radiolabeled LDL consistent with damaging effect of the variant (< 2% LDLR activity).The third is permformed on Heterologous cells (COS-7). FACS, CLSM and WB results in 24% LDLR expression and 21% LDL clearance. LDLR is retained in the ER. PS4 - Variant meets PM2 and is identified in 13 index cases who fulfil SB criteria for FH (n=1 CGMC, UFGOD, APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière; n=1 Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge; n=1 Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation)) or DLCN criteria for FH (n=1 Robarts Research Institute; n=9 CGMC, UFGOD, APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière). PP1_Strong - Variant segregate with FH in 10 informatives meiosis (6 relatives positive LDL-C > 75th percentile and 4 relatives negative LDLC < 50th percentile) from 2 families from Laboratory of Genetics and Molecular Cardiology, University of São Paulo and in 1 relative positive for variant (LDL-C > 75th percentile) from Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge. PP4 - Variant meets PM2 and is identified in 13 index cases who fulfil SB criteria for FH (n=1 CGMC, UFGOD, APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière; n=1 Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge; n=1 Molecular Genetics Laboratory (Centre for Cardiovascular Surgery and Transplantation)) or DLCN criteria for FH (n=1 Robarts Research Institute; n=9 CGMC, UFGOD, APHP.Sorbonne Université, Hôpital de la Pitié-Salpêtrière).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 1, 2024