ClinVar Miner

Submissions for variant NM_017890.4(VPS13B):c.5681C>T (p.Thr1894Met) (rs117148013)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000718312 SCV000849174 likely benign History of neurodevelopmental disorder 2017-04-14 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: In silico models in agreement (benign) ,Other data supporting benign classification
Athena Diagnostics Inc RCV000711299 SCV000841639 uncertain significance not provided 2018-05-15 criteria provided, single submitter clinical testing
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000515167 SCV000744233 likely benign Cohen syndrome 2015-09-21 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000711299 SCV000229738 uncertain significance not provided 2015-03-11 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000515167 SCV000611530 uncertain significance Cohen syndrome 2017-05-23 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000194012 SCV000249412 uncertain significance not specified 2015-04-02 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000515167 SCV000743190 benign Cohen syndrome 2014-10-09 criteria provided, single submitter clinical testing
Invitae RCV000515167 SCV000755396 uncertain significance Cohen syndrome 2018-11-09 criteria provided, single submitter clinical testing This sequence change replaces threonine with methionine at codon 1894 of the VPS13B protein (p.Thr1894Met). The threonine residue is weakly conserved and there is a moderate physicochemical difference between threonine and methionine. This variant is present in population databases (rs117148013, ExAC 0.1%). This variant has not been reported in the literature in individuals with VPS13B-related disease. ClinVar contains an entry for this variant (Variation ID: 196918). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.

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