ClinVar Miner

Submissions for variant NM_000527.5(LDLR):c.638G>C (p.Ser213Thr)

dbSNP: rs879254604
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
LDLR-LOVD, British Heart Foundation RCV000237432 SCV000294837 likely benign Hypercholesterolemia, familial, 1 2016-03-25 criteria provided, single submitter literature only
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000454439 SCV000539521 uncertain significance not specified 2016-10-31 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: This variant is not present in ExAC. It was seen in one patient with FH. It is classified in ClinVar with 1 star as Likely Benign by The British Heart Foundation. The region is not conserved but no species have a Thr at this position.
Invitae RCV001833252 SCV000544655 uncertain significance Familial hypercholesterolemia 2021-08-12 criteria provided, single submitter clinical testing This sequence change replaces serine with threonine at codon 213 of the LDLR protein (p.Ser213Thr). The serine residue is highly conserved and there is a small physicochemical difference between serine and threonine. This variant is not present in population databases (ExAC no frequency). This missense change has been observed in individual(s) with either definite or probable familial hypercholesterolemia (PMID: 16389549). This variant is also known as p.Ser192Thr. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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.
Color Diagnostics, LLC DBA Color Health RCV001833252 SCV004358487 uncertain significance Familial hypercholesterolemia 2023-07-27 criteria provided, single submitter clinical testing This missense variant (also known as p.Ser192Thr in the mature protein) replaces serine with threonine at codon 213 of the LDLR protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with familial hypercholesterolemia (PMID: 16389549, 18325082). This variant has been identified in 1/250886 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
All of Us Research Program, National Institutes of Health RCV000237432 SCV004820188 uncertain significance Hypercholesterolemia, familial, 1 2023-11-20 criteria provided, single submitter clinical testing This missense variant (also known as p.Ser192Thr in the mature protein) replaces serine with threonine at codon 213 of the LDLR protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with familial hypercholesterolaemia (PMID: 16389549, 18325082). This variant has been identified in 1/250886 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Natera, Inc. RCV001833252 SCV002086374 uncertain significance Familial hypercholesterolemia 2020-02-06 no assertion criteria provided clinical testing

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