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NM_000527.5(LDLR):c.1951G>A (p.Asp651Asn) AND not provided

Germline classification:
Likely pathogenic (3 submissions)
Last evaluated:
Jan 1, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000162005.17

Allele description

NM_000527.5(LDLR):c.1951G>A (p.Asp651Asn)

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.1951G>A (p.Asp651Asn)
Other names:
NM_000527.5(LDLR):c.1951G>A
HGVS:
  • NC_000019.10:g.11120197G>A
  • NG_009060.1:g.35817G>A
  • NM_000527.5:c.1951G>AMANE SELECT
  • NM_001195798.2:c.1951G>A
  • NM_001195799.2:c.1828G>A
  • NM_001195800.2:c.1447G>A
  • NM_001195803.2:c.1570G>A
  • NP_000518.1:p.Asp651Asn
  • NP_000518.1:p.Asp651Asn
  • NP_001182727.1:p.Asp651Asn
  • NP_001182728.1:p.Asp610Asn
  • NP_001182729.1:p.Asp483Asn
  • NP_001182732.1:p.Asp524Asn
  • LRG_274t1:c.1951G>A
  • LRG_274:g.35817G>A
  • LRG_274p1:p.Asp651Asn
  • NC_000019.9:g.11230873G>A
  • NM_000527.4:c.1951G>A
  • c.1951G>A
Protein change:
D483N
Links:
LDLR-LOVD, British Heart Foundation: LDLR_000851; dbSNP: rs730882110
NCBI 1000 Genomes Browser:
rs730882110
Molecular consequence:
  • NM_000527.5:c.1951G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195798.2:c.1951G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195799.2:c.1828G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195800.2:c.1447G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195803.2:c.1570G>A - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
no known functional consequence - Comment(s)
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000189580Dept. of Genetics and Pharmacogenomics, Merck Research Labs
no classification provided

(in vitro)
not providednot applicablein vitro

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

SCV001151670CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely pathogenic
(Jan 1, 2024)
germlineclinical testing

Citation Link,

SCV005078485GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely pathogenic
(Dec 11, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providednot applicablenot applicablenot providednot providednot providednot providednot providedin vitro
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Systematic cell-based phenotyping of missense alleles empowers rare variant association studies: a case for LDLR and myocardial infarction.

Thormaehlen AS, Schuberth C, Won HH, Blattmann P, Joggerst-Thomalla B, Theiss S, Asselta R, Duga S, Merlini PA, Ardissino D, Lander ES, Gabriel S, Rader DJ, Peloso GM, Pepperkok R, Kathiresan S, Runz H.

PLoS Genet. 2015 Feb;11(2):e1004855. doi: 10.1371/journal.pgen.1004855. Erratum in: PLoS Genet. 2015 Mar 17;11(3):e1005060. doi: 10.1371/journal.pgen.1005060.

PubMed [citation]
PMID:
25647241
PMCID:
PMC4409815

Details of each submission

From Dept. of Genetics and Pharmacogenomics, Merck Research Labs, SCV000189580.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedin vitro PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not applicablenot applicablenot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV001151670.17

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

LDLR: PM2, PM5, PS4:Moderate

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV005078485.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as D630N; This variant is associated with the following publications: (PMID: 15241806, 25647241, 29396260, 30312929, 25487149)

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

Last Updated: Sep 29, 2024