ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.1298+6G>A

gnomAD frequency: 0.00010  dbSNP: rs578207030
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000127490 SCV000171065 benign not specified 2013-10-21 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000460234 SCV000549897 uncertain significance Developmental and epileptic encephalopathy, 12 2022-10-13 criteria provided, single submitter clinical testing This sequence change falls in intron 14 of the PNKP gene. It does not directly change the encoded amino acid sequence of the PNKP protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs578207030, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with PNKP-related conditions. ClinVar contains an entry for this variant (Variation ID: 138721). 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 is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
New York Genome Center RCV001588978 SCV001815820 uncertain significance Ataxia - oculomotor apraxia type 4 2020-09-09 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004544279 SCV004771860 likely benign PNKP-related disorder 2019-07-10 criteria provided, single submitter 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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