NM_000527.4(LDLR):c.-120C>T AND Familial hypercholesterolemia 1

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Likely pathogenic(2) (Last evaluated: Mar 27, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
5 submissions [Details]
Record status:
current
Accession:
RCV000211703.6

Allele description [Variation Report for NM_000527.4(LDLR):c.-120C>T]

NM_000527.4(LDLR):c.-120C>T

Genes:
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
LDLR-AS1:LDLR antisense RNA 1 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_000527.4(LDLR):c.-120C>T
HGVS:
  • NC_000019.10:g.11089429C>T
  • NG_009060.1:g.5049C>T
  • NG_009060.1:g.5049C>T
  • LRG_274t1:c.-120C>T
  • LRG_274:g.5049C>T
  • NC_000019.9:g.11200105C>T
  • NC_000019.9:g.11200105C>T
  • NM_000527.4:c.-120C>T
  • NR_163945.1:n.231G>A
  • c.-120C>T
Links:
LDLR-LOVD, British Heart Foundation: LDLR_001115; dbSNP: rs875989886
NCBI 1000 Genomes Browser:
rs875989886
Molecular consequence:
  • NR_163945.1:n.231G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
2

Condition(s)

Name:
Familial hypercholesterolemia 1 (FHCL1)
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
SCV000268529Cardiovascular Genetics Laboratory,PathWest Laboratory Medicine WA - Fiona Stanley Hospitalno assertion criteria providedPathogenic
(Apr 17, 2015)
germlineclinical testing

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

SCV000294395LDLR-LOVD, British Heart Foundationcriteria provided, single submitter
Likely pathogenic
(Mar 25, 2016)
germlineliterature only

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

Citation Link,

SCV000540711Molecular Genetics Laboratory,Centre for Cardiovascular Surgery and Transplantation

See additional submitters

criteria provided, single submitter
Likely benign
(Mar 27, 2017)
inherited, unknownclinical testing, in vitro

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

SCV000605987Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde,Academisch Medisch Centrumno assertion criteria providedPathogenicgermlineresearch

SCV000607395Fundacion Hipercolesterolemia Familiar - SAFEHEARTcriteria provided, single submitter
Likely pathogenic
(Mar 1, 2016)
germlineresearch

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes5not providednot provided4not providedclinical testing, literature only
not providedgermlineunknownnot providednot providednot providednot providednot providedresearch
not providedunknownyesnot providednot providednot providednot providednot providedin vitro
Caucasianinheritedyes22not provided3976not providedclinical testing

Citations

PubMed

Genetic diagnosis of familial hypercholesterolemia using a DNA-array based platform.

Alonso R, Defesche JC, Tejedor D, Castillo S, Stef M, Mata N, Gomez-Enterria P, Martinez-Faedo C, Forga L, Mata P.

Clin Biochem. 2009 Jun;42(9):899-903. doi: 10.1016/j.clinbiochem.2009.01.017. Epub 2009 Feb 6.

PubMed [citation]
PMID:
19318025

The molecular basis of familial hypercholesterolemia in the Czech Republic: spectrum of LDLR mutations and genotype-phenotype correlations.

Tichý L, Freiberger T, Zapletalová P, Soška V, Ravčuková B, Fajkusová L.

Atherosclerosis. 2012 Aug;223(2):401-8. doi: 10.1016/j.atherosclerosis.2012.05.014. Epub 2012 May 23.

PubMed [citation]
PMID:
22698793
See all PubMed Citations (4)

Details of each submission

From Cardiovascular Genetics Laboratory,PathWest Laboratory Medicine WA - Fiona Stanley Hospital, SCV000268529.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences

From LDLR-LOVD, British Heart Foundation, SCV000294395.2

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

From Molecular Genetics Laboratory,Centre for Cardiovascular Surgery and Transplantation, SCV000540711.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedin vitro PubMed (3)
2Caucasian2not providednot providedclinical testing PubMed (3)

Description

"A functional analysis has been previously published (Francova et al, 2004). Only 3% of activity in comparing with wt promoter."

Description

A functional analysis was previously published (Francova et al, 2004). Only 3% of activity in comparing with wt promoter.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providedassert pathogenicitynot providednot providednot providednot provided
2inheritedyes3976Whole bloodnot provided2not provided2not provided

From Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde,Academisch Medisch Centrum, SCV000605987.1

#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, SCV000607395.1

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

Description

"Heterologous cells (HepG2), luciferase assays"
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided
2germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 4, 2021

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