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NM_000527.5(LDLR):c.394C>T (p.Arg132Trp) AND Familial hypercholesterolemia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 31, 2021
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:
RCV001988908.5

Allele description [Variation Report for NM_000527.5(LDLR):c.394C>T (p.Arg132Trp)]

NM_000527.5(LDLR):c.394C>T (p.Arg132Trp)

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.394C>T (p.Arg132Trp)
HGVS:
  • NC_000019.10:g.11105300C>T
  • NG_009060.1:g.20920C>T
  • NM_000527.5:c.394C>TMANE SELECT
  • NM_001195798.2:c.394C>T
  • NM_001195799.2:c.271C>T
  • NM_001195800.2:c.314-2092C>T
  • NM_001195803.2:c.314-1265C>T
  • NP_000518.1:p.Arg132Trp
  • NP_001182727.1:p.Arg132Trp
  • NP_001182728.1:p.Arg91Trp
  • LRG_274:g.20920C>T
  • NC_000019.9:g.11215976C>T
Protein change:
R132W
Links:
dbSNP: rs368978979
NCBI 1000 Genomes Browser:
rs368978979
Molecular consequence:
  • NM_001195800.2:c.314-2092C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195803.2:c.314-1265C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000527.5:c.394C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195798.2:c.394C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001195799.2:c.271C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Familial hypercholesterolemia
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
SCV002278672Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Aug 31, 2021)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Homozygous Familial Hypercholesterolemia in Spain: Prevalence and Phenotype-Genotype Relationship.

Sánchez-Hernández RM, Civeira F, Stef M, Perez-Calahorra S, Almagro F, Plana N, Novoa FJ, Sáenz-Aranzubía P, Mosquera D, Soler C, Fuentes FJ, Brito-Casillas Y, Real JT, Blanco-Vaca F, Ascaso JF, Pocovi M.

Circ Cardiovasc Genet. 2016 Dec;9(6):504-510. doi: 10.1161/CIRCGENETICS.116.001545. Epub 2016 Oct 26.

PubMed [citation]
PMID:
27784735

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002278672.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change replaces arginine with tryptophan at codon 132 of the LDLR protein (p.Arg132Trp). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is present in population databases (rs368978979, ExAC 0.002%). This missense change has been observed in individual(s) with familial hypercholesterolemia (PMID: 27784735). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The tryptophan amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024