ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.477+2T>G (rs758014228)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Praxis fuer Humangenetik Tuebingen RCV000658500 SCV000780268 likely pathogenic not provided 2018-02-28 criteria provided, single submitter clinical testing
Invitae RCV000702718 SCV000831584 likely pathogenic Parkinson disease 9; Spastic paraplegia 78, autosomal recessive 2018-04-04 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 5 of the ATP13A2 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is present in population databases (rs758014228, ExAC 0.009%). This variant has not been reported in the literature in individuals with ATP13A2-related disease. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ATP13A2 are known to be pathogenic (PMID: 16964263, 21696388). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Athena Diagnostics Inc RCV000658500 SCV000841009 uncertain significance not provided 2018-02-14 criteria provided, single submitter clinical testing
Ambry Genetics RCV000720496 SCV000851373 likely pathogenic History of neurodevelopmental disorder 2018-01-26 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Alterations at the canonical donor/acceptor sites (+/- 1, 2) without splicing assay data in support of pathogenicity,In silico models in agreement (deleterious) and/or completely conserved position in appropriate species

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