ClinVar Miner

Submissions for variant NM_152564.5(VPS13B):c.1559A>G (p.His520Arg)

gnomAD frequency: 0.00068  dbSNP: rs143205296
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000426832 SCV000225382 uncertain significance not provided 2015-04-07 criteria provided, single submitter clinical testing
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia RCV000239145 SCV000297277 uncertain significance not specified 2015-11-10 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000375746 SCV000470768 uncertain significance Cohen syndrome 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.
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000426832 SCV000511792 likely benign not provided 2016-12-09 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV000375746 SCV000755419 likely benign Cohen syndrome 2024-01-29 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000426832 SCV000780921 uncertain significance not provided 2018-07-01 criteria provided, single submitter clinical testing
Baylor Genetics RCV000375746 SCV001529778 uncertain significance Cohen syndrome 2018-01-01 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Genome-Nilou Lab RCV000375746 SCV001652732 uncertain significance Cohen syndrome 2021-05-18 criteria provided, single submitter clinical testing
GeneDx RCV000426832 SCV001823659 likely benign not provided 2018-08-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV002399624 SCV002704401 uncertain significance Inborn genetic diseases 2020-01-29 criteria provided, single submitter clinical testing The p.H520R variant (also known as c.1559A>G), located in coding exon 10 of the VPS13B gene, results from an A to G substitution at nucleotide position 1559. The histidine at codon 520 is replaced by arginine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV000375746 SCV003820423 uncertain significance Cohen syndrome 2022-06-08 criteria provided, single submitter clinical testing
Natera, Inc. RCV000375746 SCV001454806 likely benign Cohen syndrome 2020-09-16 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV003982923 SCV004796295 likely benign VPS13B-related disorder 2022-01-28 no assertion criteria provided 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).

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