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NM_000527.5(LDLR):c.337G>T (p.Glu113Ter) AND Hypercholesterolemia, familial, 1

Germline classification:
Pathogenic/Likely pathogenic (11 submissions)
Last evaluated:
May 24, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000211560.16

Allele description [Variation Report for NM_000527.5(LDLR):c.337G>T (p.Glu113Ter)]

NM_000527.5(LDLR):c.337G>T (p.Glu113Ter)

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.337G>T (p.Glu113Ter)
Other names:
FH Paris-5; NP_000518.1:p.E113*
HGVS:
  • NC_000019.10:g.11105243G>T
  • NG_009060.1:g.20863G>T
  • NM_000527.5:c.337G>TMANE SELECT
  • NM_001195798.2:c.337G>T
  • NM_001195799.2:c.214G>T
  • NM_001195800.2:c.314-2149G>T
  • NM_001195803.2:c.314-1322G>T
  • NP_000518.1:p.Glu113Ter
  • NP_000518.1:p.Glu113Ter
  • NP_001182727.1:p.Glu113Ter
  • NP_001182728.1:p.Glu72Ter
  • LRG_274t1:c.337G>T
  • LRG_274:g.20863G>T
  • LRG_274p1:p.Glu113Ter
  • NC_000019.9:g.11215919G>T
  • NM_000527.4:c.337G>T
  • c.337G>T
  • p.(Glu113*)
  • p.Glu113*
Protein change:
E113*
Links:
LDLR-LOVD, British Heart Foundation: LDLR_001705;
Molecular consequence:
  • NM_001195800.2:c.314-2149G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195803.2:c.314-1322G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000527.5:c.337G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001195798.2:c.337G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001195799.2:c.214G>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
14

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000268558Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital
no assertion criteria provided
Pathogenic
(May 28, 2013)
germlineclinical testing

SCV000294637LDLR-LOVD, British Heart Foundation
criteria provided, single submitter

(ACGS Guidelines, 2013)
Pathogenic
(Mar 25, 2016)
germlineliterature only

PubMed (5)
[See all records that cite these PMIDs]

Citation Link,

SCV000484731Robarts 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]

SCV000503142Centre 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]

SCV000583663U4M - 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]

SCV000588497Laboratory of Genetics and Molecular Cardiology, University of São Paulo - HipercolBrasil
criteria provided, single submitter

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

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

SCV000606090Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum
no assertion criteria provided
Pathogenicgermlineresearch

SCV000748084Iberoamerican FH Network
criteria provided, single submitter

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

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

SCV001432646Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 11, 2019)
germlineresearch

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

SCV001653587Laboratory of molecular diagnosis of dyslipidemias, Università egli studi di Napoli Federico II
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 24, 2021)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV002769519Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 6, 2021)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes4214not provided2606not providedclinical testing, literature only, research
not providedgermlineunknownnot providednot providednot providednot providednot providedresearch
Caucasiangermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Genetic investigation of patients with hypercholesterolemia type IIa.

Szalai C, Császár A, Czinner A, Palicz T, Halmos B, Romics L.

Clin Genet. 1999 Jan;55(1):67-8. No abstract available.

PubMed [citation]
PMID:
10066037

Spectrum of LDL receptor gene mutations in Denmark: implications for molecular diagnostic strategy in heterozygous familial hypercholesterolemia.

Jensen HK, Jensen LG, Meinertz H, Hansen PS, Gregersen N, Faergeman O.

Atherosclerosis. 1999 Oct;146(2):337-44.

PubMed [citation]
PMID:
10532689
See all PubMed Citations (12)

Details of each submission

From Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital, SCV000268558.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences

From LDLR-LOVD, British Heart Foundation, SCV000294637.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedliterature only PubMed (5)
2not provided1not providednot providedliterature only PubMed (5)
3not provided1not providednot providedliterature only PubMed (5)
4not provided1not providednot providedliterature only PubMed (5)
5not provided1not providednot providedliterature only PubMed (5)
#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

From Robarts Research Institute, Western University, SCV000484731.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not 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, SCV000503142.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided11not providednot providedclinical testing PubMed (1)

Description

subjects mutated among 2600 FH index cases screened = 11 , family members = 8 with co-segregation

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes2600not providednot provided11not providednot providednot provided

From U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille, SCV000583663.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided19not providednot providedclinical testing PubMed (1)

Description

Dutch Lipid Clinic Scoring : Definite FH

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided19not provided14not provided

From Laboratory of Genetics and Molecular Cardiology, University of São Paulo - HipercolBrasil, SCV000588497.1

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

Description

"Assay description:Comp Htz (with p.(Glu228Lys)) patients' fibroblasts, 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, SCV000606090.1

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

From Iberoamerican FH Network, SCV000748084.1

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

Description

"Assay Description:Comp Htz (with p.(Glu228Lys)) patients' fibroblasts, 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 Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia, SCV001432646.1

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

From Laboratory of molecular diagnosis of dyslipidemias, Università egli studi di Napoli Federico II, SCV001653587.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Caucasian1not providednot providedclinical testing PubMed (4)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002769519.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, 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 1 and LDL cholesterol level QTL2 (MIM#143890). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance (GeneReviews). (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (SP) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity (ClinVar, DECIPHER). (SP) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported in many patients with familial hypercholesterolemia (ClinVar), both heterozygous (PMID:28502510) and homozygous (PMID:26894473). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: Sep 29, 2024