ClinVar Miner

Submissions for variant NM_017890.4(VPS13B):c.11146G>A (p.Ala3716Thr) (rs142476821)

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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000081872 SCV000113807 benign not specified 2014-04-15 criteria provided, single submitter clinical testing
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia RCV000081872 SCV000297276 likely benign not specified 2015-11-16 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000361059 SCV000470859 likely benign Cohen syndrome 2018-01-12 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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Genetic Services Laboratory, University of Chicago RCV000081872 SCV000597900 benign not specified 2018-04-10 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000710109 SCV000616264 likely benign not provided 2018-02-14 criteria provided, single submitter clinical testing
Invitae RCV000361059 SCV000630857 benign Cohen syndrome 2020-11-27 criteria provided, single submitter clinical testing
GeneDx RCV000710109 SCV000715025 likely benign not provided 2018-11-30 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 23352163)
Ambry Genetics RCV000718321 SCV000849183 uncertain significance History of neurodevelopmental disorder 2018-09-09 criteria provided, single submitter clinical testing The p.A3716T variant (also known as c.11146G>A), located in coding exon 57 of the VPS13B gene, results from a G to A substitution at nucleotide position 11146. The alanine at codon 3716 is replaced by threonine, an amino acid with similar properties. In one study, this variant was compound heterozygous with another VPS13B missense alteration in an individual with autism and facial features, limbs, and hair growth pattern known to characterize Cohen syndrome (Yu TW et al. Neuron, 2013 Jan;77:259-73). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on available evidence to date, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV000361059 SCV001454477 likely benign Cohen syndrome 2020-01-14 no assertion criteria provided clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000710109 SCV001739589 likely benign not provided no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000710109 SCV001797896 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000710109 SCV001920003 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000710109 SCV001929814 likely benign not provided no assertion criteria provided clinical testing

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