NM_000527.4(LDLR):c.2089G>A (p.Ala697Thr) AND Familial hypercholesterolemia

Clinical significance:Uncertain significance (Last evaluated: Mar 12, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001192332.1

Allele description [Variation Report for NM_000527.4(LDLR):c.2089G>A (p.Ala697Thr)]

NM_000527.4(LDLR):c.2089G>A (p.Ala697Thr)

Gene:
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.2089G>A (p.Ala697Thr)
HGVS:
  • NC_000019.10:g.11120471G>A
  • NG_009060.1:g.36091G>A
  • NM_000527.4:c.2089G>A
  • NM_001195798.2:c.2089G>A
  • NM_001195799.2:c.1966G>A
  • NM_001195800.2:c.1585G>A
  • NM_001195803.2:c.1606+238G>A
  • NP_000518.1:p.Ala697Thr
  • NP_001182727.1:p.Ala697Thr
  • NP_001182728.1:p.Ala656Thr
  • NP_001182729.1:p.Ala529Thr
  • LRG_274t1:c.2089G>A
  • LRG_274:g.36091G>A
  • LRG_274p1:p.Ala697Thr
  • NC_000019.9:g.11231147G>A
Protein change:
A529T
Links:
dbSNP: rs776217028
NCBI 1000 Genomes Browser:
rs776217028
Molecular consequence:
  • NM_001195803.2:c.1606+238G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000527.4:c.2089G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195798.2:c.2089G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195799.2:c.1966G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195800.2:c.1585G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001360364Color Health, Inccriteria provided, single submitter
Uncertain significance
(Mar 12, 2019)
germlineclinical testing

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

Description

Variant of Uncertain Significance due to insufficient evidence: This missense variant (also known as p.Ala676Thr in the mature protein) replaces alanine with threonine at codon 697 of the LDLR protein. Computational prediction tools and conservation analyses are inconclusive regarding the impact of this variant on the protein function. Computational splicing tools suggest that this variant may not impact RNA splicing. To our knowledge, functional assays have not been performed for this variant nor has this variant been reported in individuals affected with familial hypercholesterolemia in the literature. This variant has been identified in 1/245924 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Available evidence is insufficient to determine the role of this variant in disease conclusively.

SCV001360364

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, SCV001360364.1

#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: Apr 12, 2021

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