NM_000527.5(LDLR):c.1359-5C>G AND Familial hypercholesterolemia 1

Clinical significance:Conflicting interpretations of pathogenicity, Pathogenic(1);Uncertain significance(2) (Last evaluated: Oct 12, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000238316.4

Allele description [Variation Report for NM_000527.5(LDLR):c.1359-5C>G]

NM_000527.5(LDLR):c.1359-5C>G

Genes:
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
MIR6886:microRNA 6886 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_000527.5(LDLR):c.1359-5C>G
HGVS:
  • NC_000019.10:g.11113530C>G
  • NG_009060.1:g.29150C>G
  • NM_000527.5:c.1359-5C>GMANE SELECT
  • NM_001195798.2:c.1359-5C>G
  • NM_001195799.2:c.1236-5C>G
  • NM_001195800.2:c.855-5C>G
  • NM_001195803.2:c.978-5C>G
  • LRG_274t1:c.1359-5C>G
  • LRG_274:g.29150C>G
  • NC_000019.9:g.11224206C>G
  • NM_000527.4:c.1359-5C>G
  • NR_106946.1:n.57C>G
  • c.1359-5C>G
Links:
LDLR-LOVD, British Heart Foundation: LDLR_000192; dbSNP: rs531005522
NCBI 1000 Genomes Browser:
rs531005522
Molecular consequence:
  • NM_000527.5:c.1359-5C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195798.2:c.1359-5C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195799.2:c.1236-5C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195800.2:c.855-5C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195803.2:c.978-5C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NR_106946.1:n.57C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000295389LDLR-LOVD, British Heart Foundationcriteria provided, single submitter
Pathogenic
(Mar 25, 2016)
germlineliterature only

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

Citation Link,

SCV000322946Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorgecriteria provided, single submitter
Uncertain significance
(Mar 1, 2016)
germlineresearch

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

SCV001286369Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Oct 12, 2017)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes1not providednot provided1not providedresearch, literature only

Citations

PubMed

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; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Low-density lipoprotein receptor gene familial hypercholesterolemia variant database: update and pathological assessment.

Usifo E, Leigh SE, Whittall RA, Lench N, Taylor A, Yeats C, Orengo CA, Martin AC, Celli J, Humphries SE.

Ann Hum Genet. 2012 Sep;76(5):387-401. doi: 10.1111/j.1469-1809.2012.00724.x.

PubMed [citation]
PMID:
22881376
See all PubMed Citations (5)

Details of each submission

From LDLR-LOVD, British Heart Foundation, SCV000295389.2

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

From Cardiovascular Research Group,Instituto Nacional de Saude Doutor Ricardo Jorge, SCV000322946.1

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

Description

"Heterozygous patients' lymphocytes, RNA assays"

Description

0/75 normolipidaemic Portuguese controls

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

From Illumina Clinical Services Laboratory,Illumina, SCV001286369.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

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

Last Updated: Nov 27, 2021

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