ClinVar Miner

Submissions for variant NM_001128159.3(VPS53):c.1312_1313+2del

gnomAD frequency: 0.00003  dbSNP: rs768997239
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000669688 SCV000794465 likely pathogenic Pontocerebellar hypoplasia type 2E 2017-09-27 criteria provided, single submitter clinical testing
GeneDx RCV001662736 SCV001874199 likely pathogenic not provided 2022-09-14 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); Canonical splice site variant in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001731871 SCV001983532 likely pathogenic Pontoneocerebellar hypoplasia 2021-09-17 criteria provided, single submitter clinical testing Variant summary: VPS53 c.1312_1313+2delAAGT is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 5` splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 2.8e-05 in 251362 control chromosomes (gnomAD). To our knowledge, no occurrence of c.1312_1313+2delAAGT in individuals affected with Pontocerebellar Hypoplasia, Type 2E and no experimental evidence demonstrating its impact on protein function have been reported. One ClinVar submitter (evaluation after 2014) cites the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000669688 SCV002811487 likely pathogenic Pontocerebellar hypoplasia type 2E 2022-04-05 criteria provided, single submitter clinical testing

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