ClinVar Miner

Submissions for variant NM_007217.4(PDCD10):c.474+5G>A

gnomAD frequency: 0.00001  dbSNP: rs1553759139
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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 RCV000560557 SCV000644919 pathogenic Cerebral cavernous malformation 3 2023-09-10 criteria provided, single submitter clinical testing This sequence change falls in intron 6 of the PDCD10 gene. It does not directly change the encoded amino acid sequence of the PDCD10 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with cerebral cavernous malformation (PMID: 16329096, 24466005, 25122144). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 468331). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV000626904 SCV000747607 likely pathogenic Cerebral arteriovenous malformation; Seizure; Hemiparesis; Cavernous hemangioma 2017-01-01 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000721806 SCV000852947 pathogenic not provided 2016-11-21 criteria provided, single submitter clinical testing
GeneDx RCV000721806 SCV002056038 pathogenic not provided 2022-07-13 criteria provided, single submitter clinical testing Non-canonical splice site variant demonstrated to result in loss-of-function (Liquori CL, 2006); De novo variant with confirmed parentage in a patient referred for genetic testing at GeneDx; however, the reported clinical features are only partially consistent with the features typically observed in individuals with pathogenic variants in this gene; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 28116327, 30904992, 24466005, 25122144, 16329096)
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV003380616 SCV004098669 pathogenic Hereditary cavernous hemangioma of brain 2023-10-24 criteria provided, single submitter clinical testing
Baylor Genetics RCV000560557 SCV000853248 pathogenic Cerebral cavernous malformation 3 2018-11-23 no assertion criteria provided clinical testing

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