ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.2885C>T (p.Thr962Met)

gnomAD frequency: 0.00003  dbSNP: rs547184348
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000903289 SCV001047748 benign Cohen syndrome 2024-01-27 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000903289 SCV001325903 uncertain significance Cohen syndrome 2018-01-15 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.
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital RCV000903289 SCV001984485 likely benign Cohen syndrome 2020-11-23 criteria provided, single submitter clinical testing
Ambry Genetics RCV002434194 SCV002747128 uncertain significance Inborn genetic diseases 2018-06-20 criteria provided, single submitter clinical testing The p.T962M variant (also known as c.2885C>T), located in coding exon 19 of the VPS13B gene, results from a C to T substitution at nucleotide position 2885. The threonine at codon 962 is replaced by methionine, an amino acid with similar properties. This amino acid position is not well conserved in available vertebrate species, and methionine is the reference amino acid in other vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV003910787 SCV004719552 likely benign VPS13B-related disorder 2022-01-28 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV000903289 SCV001454821 benign Cohen syndrome 2020-09-16 no assertion criteria provided clinical testing

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