ClinVar Miner

Submissions for variant NM_015627.2(LDLRAP1):c.605C>A (p.Ser202Tyr) (rs121908326)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Integrated Genetics/Laboratory Corporation of America RCV000587646 SCV000699408 uncertain significance not provided 2017-06-02 criteria provided, single submitter clinical testing Variant summary: The c.605C>A (p.Ser202Tyr) in LDLRAP1gene is a missense change that involves a non-conserved nucleotide. The variant is located outside of any known domain or repeat. 4/4 in silico tools predict damaging outcome (SNP&GO not captured due to low reliability index), however no functional studies supporting these predictions were published at the time of evaluation. The variant is present in the large control population dataset of ExAC at a frequency of 0.001165 (140/ 120202 chrs tested), which exceeds the maximal expected frequency of a pathogenic allele (0.00079) in this gene. However, in ExAC, this variant is identified in cis with c.604T>C leading to the c.604_605delinsCA (p.Ser202His) in 73 individuals (~50%), altering its functional interpretation. The c.605C>A was identified heterozygously in affected individual without strong evidence for causality. One reputable database/clinical laboratory cite the variant with an outdated classification. Taking all lines of evidence into consideration, the variant was classified as VUS-Possibly Benign until more information becomes available.
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease,Montreal Heart Institute RCV000005042 SCV000987666 uncertain significance Familial hypercholesterolemia 4 criteria provided, single submitter clinical testing
Invitae RCV000005042 SCV001031361 likely benign Familial hypercholesterolemia 4 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000005042 SCV001259183 benign Familial hypercholesterolemia 4 2017-07-27 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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
OMIM RCV000005042 SCV000025218 pathogenic Familial hypercholesterolemia 4 2001-05-18 no assertion criteria provided literature only

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