ClinVar Miner

Submissions for variant NC_000017.10:g.(465986_489509)_(489605_505034)dup

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003994998 SCV004813786 likely pathogenic Pontoneocerebellar hypoplasia 2024-02-23 criteria provided, single submitter clinical testing Variant summary: The variant involves the duplication of exon 13 in the VPS53 gene. It is assumed to be a tandem duplication in direct orientation (PMIDs: 25640679, 30054569). This Copy Number Variant (CNV) is expected to alter the reading frame and predicted to result in a truncation or absence of the encoded protein due to nonsense mediated decay (NMD). A presumed nomenclature of c.(1218+1_1219-1)_(1313+1_1314-1)dup has been designated for the purposes of this classification. The variant was absent in 20442 control chromosomes (gnomAD structural variants dataset). To our knowledge, no occurrence of c.(1218+1_1219-1)_(1313+1_1314-1)dup in individuals affected with Pontocerebellar Hypoplasia, Type 2E and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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