NM_000527.5(LDLR):c.115T>C (p.Cys39Arg) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 14, 2023
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:
RCV003736799.1

Allele description [Variation Report for NM_000527.5(LDLR):c.115T>C (p.Cys39Arg)]

NM_000527.5(LDLR):c.115T>C (p.Cys39Arg)

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.115T>C (p.Cys39Arg)
HGVS:
  • NC_000019.10:g.11100270T>C
  • NG_009060.1:g.15890T>C
  • NM_000527.5:c.115T>CMANE SELECT
  • NM_001195798.2:c.115T>C
  • NM_001195799.2:c.115T>C
  • NM_001195800.2:c.115T>C
  • NM_001195803.2:c.115T>C
  • NP_000518.1:p.Cys39Arg
  • NP_000518.1:p.Cys39Arg
  • NP_001182727.1:p.Cys39Arg
  • NP_001182728.1:p.Cys39Arg
  • NP_001182729.1:p.Cys39Arg
  • NP_001182732.1:p.Cys39Arg
  • LRG_274t1:c.115T>C
  • LRG_274:g.15890T>C
  • LRG_274p1:p.Cys39Arg
  • NC_000019.9:g.11210946T>C
  • NM_000527.4:c.115T>C
Protein change:
C39R
Links:
dbSNP: rs1555802275
NCBI 1000 Genomes Browser:
rs1555802275
Molecular consequence:
  • NM_000527.5:c.115T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195798.2:c.115T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195799.2:c.115T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195800.2:c.115T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195803.2:c.115T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004563571ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)		Uncertain significance
(Nov 14, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV004563571.1

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

Description

The LDLR c.115T>C; p.Cys39Arg variant (rs1555802275) is reported in the literature in an individual as part of a carrier screen (Grzymski 2020). This variant is reported in ClinVar (Variation ID: 440543) and is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.961). This variant is located at a highly conserved cysteine residue involved in disulfide bond formation critical for proper protein folding and stability (Daly 1995). However, given the lack of clinical and functional data, the significance of this variant is uncertain at this time. References: Daly NL et al. Three-dimensional structure of a cysteine-rich repeat from the low-density lipoprotein receptor. Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6334-8. PMID: 7603991. Grzymski JJ et al. Population genetic screening efficiently identifies carriers of autosomal dominant diseases. Nat Med. 2020 Aug;26(8):1235-1239. PMID: 32719484.

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

Last Updated: Sep 29, 2024