ClinVar Miner

Submissions for variant NM_001083961.2(WDR62):c.1480G>A (p.Gly494Arg)

gnomAD frequency: 0.00006  dbSNP: rs587784543
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000147915 SCV000195407 likely pathogenic Microcephaly 2, primary, autosomal recessive, with or without cortical malformations 2013-05-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000622916 SCV000741083 likely pathogenic Inborn genetic diseases 2015-10-23 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000147915 SCV001287501 uncertain significance Microcephaly 2, primary, autosomal recessive, with or without cortical malformations 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Mayo Clinic Laboratories, Mayo Clinic RCV001507436 SCV001712986 likely pathogenic not provided 2022-06-27 criteria provided, single submitter clinical testing PP1, PP4, PM2, PM3
GeneDx RCV001507436 SCV001871094 uncertain significance not provided 2022-02-07 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31589614, 33604570)
Invitae RCV001507436 SCV002210241 uncertain significance not provided 2022-02-11 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 494 of the WDR62 protein (p.Gly494Arg). This variant is present in population databases (rs587784543, gnomAD 0.01%). This missense change has been observed in individual(s) with clinical features of Seckel syndrome (PMID: 33604570). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 160249). 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: "Probably Damaging"; 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.
Diagnostic Laboratory, Strasbourg University Hospital RCV002274918 SCV002562776 likely pathogenic Abnormal cerebral morphology no assertion criteria provided clinical testing

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