NM_000527.4(LDLR):c.-101T>C AND Familial hypercholesterolemia

Clinical significance:Uncertain significance (Last evaluated: Oct 16, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001181021.1

Allele description [Variation Report for NM_000527.4(LDLR):c.-101T>C]

NM_000527.4(LDLR):c.-101T>C

Genes:
LDLR-AS1:LDLR antisense RNA 1 [Gene - HGNC]
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_000527.4(LDLR):c.-101T>C
HGVS:
  • NC_000019.10:g.11089448T>C
  • NG_009060.1:g.5068T>C
  • NG_009060.1:g.5068T>C
  • NM_000527.4:c.-101T>C
  • LRG_274t1:c.-101T>C
  • LRG_274:g.5068T>C
  • NC_000019.9:g.11200124T>C
  • NC_000019.9:g.11200124T>C
  • NR_163945.1:n.212A>G
  • c.-101T>C
Links:
LDLR-LOVD, British Heart Foundation: LDLR_000001; dbSNP: rs747068848
NCBI 1000 Genomes Browser:
rs747068848
Molecular consequence:
  • NM_000527.4:c.-101T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NR_163945.1:n.212A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Familial hypercholesterolemia (FH)
Identifiers:
MONDO: MONDO:0005439; MedGen: C0020445; OMIM: PS143890

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001346074Color Health, Inccriteria provided, single submitter
Uncertain significance
(Oct 16, 2019)
germlineclinical testing

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

Description

This variant is located in the TATA box in the promoter region of the LDLR gene. A functional study has shown that this variant decreases the promoter activity by 36% (PMID: 25248394). This variant has been reported in an individual affected with familial hypercholesterolemia (PMID: 22881376). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

SCV001346074

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

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

Details of each submission

From Color Health, Inc, SCV001346074.1

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

Last Updated: Nov 20, 2021

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