ClinVar Miner

Submissions for variant NM_000527.4(LDLR):c.1056C>T (p.Cys352=) (rs13306515)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001082978 SCV000556792 benign Familial hypercholesterolemia 2019-12-31 criteria provided, single submitter clinical testing
Color RCV000462425 SCV000689754 benign Familial hypercholesterolemia 1 2017-07-17 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000780374 SCV000917576 likely benign not specified 2017-09-22 criteria provided, single submitter clinical testing Variant summary: The LDLR c.1056C>T (p.Cys352Cys) variant involves the alteration of a non-conserved nucleotide causing a synonymous change and 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites at the locus. However, these predictions have yet to be confirmed by functional studies. This variant was found in 222/276416 control chromosomes from all ethnicities, but was observed predominantly in the East Asian subpopulation at a frequency of 0.008694 (164/18864). This frequency is about 7 times the estimated maximal expected allele frequency of a pathogenic LDLR variant (0.0012508), suggesting this is likely a benign polymorphism found primarily in the populations of East Asian origin. The variant has been identified in patients reported in the literature without strong evidence for causality. In addition, the variant has been found to co-occur with a pathogenic LDLR mutation in a patient (c.259G>T/p.W66G), supporting a benign outcome for the variant of interest (Jensen_1996). One clinical diagnostic laboratory has classified this variant as benign. Taken together, this variant is classified as likely benign, until additional studies become available (ie, clinical and/or functional studies).
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000858795 SCV001134246 benign not provided 2018-11-26 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000462425 SCV001285934 uncertain significance Familial hypercholesterolemia 1 2019-03-20 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde,Academisch Medisch Centrum RCV000462425 SCV000606303 benign Familial hypercholesterolemia 1 no assertion criteria provided research

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