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NM_000527.5(LDLR):c.269A>G (p.Asp90Gly) AND LDLR-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 26, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV003417768.4

Allele description [Variation Report for NM_000527.5(LDLR):c.269A>G (p.Asp90Gly)]

NM_000527.5(LDLR):c.269A>G (p.Asp90Gly)

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.269A>G (p.Asp90Gly)
Other names:
FH London-4; NM_000527.5(LDLR):c.269A>G
HGVS:
  • NC_000019.10:g.11102742A>G
  • NG_009060.1:g.18362A>G
  • NM_000527.5:c.269A>GMANE SELECT
  • NM_001195798.2:c.269A>G
  • NM_001195799.2:c.190+2397A>G
  • NM_001195800.2:c.269A>G
  • NM_001195803.2:c.269A>G
  • NP_000518.1:p.Asp90Gly
  • NP_000518.1:p.Asp90Gly
  • NP_001182727.1:p.Asp90Gly
  • NP_001182729.1:p.Asp90Gly
  • NP_001182732.1:p.Asp90Gly
  • LRG_274t1:c.269A>G
  • LRG_274:g.18362A>G
  • LRG_274p1:p.Asp90Gly
  • NC_000019.9:g.11213418A>G
  • NM_000527.4:c.269A>G
  • P01130:p.Asp90Gly
  • c.269A>G
Protein change:
D90G
Links:
LDLR-LOVD, British Heart Foundation: LDLR_001676; UniProtKB: P01130#VAR_005310; dbSNP: rs771019366
NCBI 1000 Genomes Browser:
rs771019366
Molecular consequence:
  • NM_001195799.2:c.190+2397A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000527.5:c.269A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195798.2:c.269A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195800.2:c.269A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195803.2:c.269A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
LDLR-related disorder
Synonyms:
LDLR-related condition
Identifiers:

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004113006PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 26, 2022)
germlineclinical testing

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

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 PreventionGenetics, part of Exact Sciences, SCV004113006.1

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

Description

The LDLR c.269A>G variant is predicted to result in the amino acid substitution p.Asp90Gly. This variant is also described using legacy nomenclature as p.Asp69Gly, has been well-documented to be pathogenic for Hypercholesterolemia (Hobbs et al. 1992. PubMed ID: 1301956; Webb et al. 1996. PubMed ID: 9026534; Day et al. 1997. PubMed ID: 9259195; Amsellem et al. 2002. PubMed ID: 12436241; Sturm et al. 2021. PubMed ID: 34037665). This variant have also been interpreted as pathogenic by the Hypercholesterolemia Variant Curation Expert Panel (https://erepo.clinicalgenome.org/evrepo/ui/interpretation/243fe145-86fd-48f6-98dd-c946485388c0). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic.

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

Last Updated: Sep 29, 2024