ClinVar Miner

Submissions for variant NM_001164617.2(GPC3):c.1354G>A (p.Val452Met) (rs11539789)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001082341 SCV000288566 benign Wilms tumor 1 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000121184 SCV000513171 likely benign not specified 2015-11-19 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000514274 SCV000610546 likely benign not provided 2017-03-09 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000514274 SCV000613539 benign not provided 2017-09-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000514274 SCV000698455 benign not provided 2016-05-05 criteria provided, single submitter clinical testing Variant summary: The GPC3 variant, c.1285G>A (p.Val429Met) causes a missense change involving a conserved nucleotide with 2/3 in silico programs (SNPs&GO and MutationTaster not captured here due to low reliability index and p-value, respectively) predict a "benign" outcome, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 511/87700 (1/171, 188 hemizygotes, 5 homozygotes), which significantly exceeds the estimated maximum expected allele frequency for a pathogenic GPC3 variant of 1/10000000. The variant of interest, to our knowledge, has not been reported in affected individuals via publications. Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
Ambry Genetics RCV000716056 SCV000846889 benign History of neurodevelopmental disorder 2016-05-04 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
ITMI RCV000121184 SCV000085352 not provided not specified 2013-09-19 no assertion provided reference population

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