ClinVar Miner

Submissions for variant NM_017890.4(VPS13B):c.1768G>A (p.Ala590Thr) (rs140601319)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000711291 SCV000225902 uncertain significance not provided 2014-10-17 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000193331 SCV000249400 uncertain significance not specified 2015-04-21 criteria provided, single submitter clinical testing
GeneDx RCV000711291 SCV000564894 uncertain significance not provided 2016-06-28 criteria provided, single submitter clinical testing The A590T variant in the VPS13B gene has been reported previously as a paternally inherited variant, found in the heterozygous state, in a patient with Cohen syndrome (Katzaki et al., 2007); no second variant was identified in the affected individual. Although not present in the homozygous state, the NHLBI ESP Exome Sequencing Project reports A590T was observed at a frequency of 0.15%, 13/8600 alleles, from individuals of European American background. The A590T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret A590T as a variant of uncertain significance.
Fulgent Genetics,Fulgent Genetics RCV000515161 SCV000611527 uncertain significance Cohen syndrome 2017-05-23 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000711291 SCV000841628 uncertain significance not provided 2017-09-27 criteria provided, single submitter clinical testing
Ambry Genetics RCV000719566 SCV000850435 uncertain significance History of neurodevelopmental disorder 2019-03-12 criteria provided, single submitter clinical testing Insufficient evidence
Invitae RCV000515161 SCV001013994 benign Cohen syndrome 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000515161 SCV001325780 likely benign Cohen syndrome 2017-04-27 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 determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille RCV001252626 SCV001428387 uncertain significance Intellectual disability 2019-01-01 no assertion criteria provided clinical testing

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