ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.416G>A (p.Arg139His) (rs34472250)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000147358 SCV000194733 uncertain significance Early infantile epileptic encephalopathy 10 2013-10-22 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000433486 SCV000203321 uncertain significance not provided 2017-12-14 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000433486 SCV000511621 uncertain significance not provided 2016-09-28 criteria provided, single submitter clinical testing Converted during submission to Uncertain significance.
GeneDx RCV000153751 SCV000514214 likely benign not specified 2017-12-18 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 RCV001086537 SCV000560526 benign Early infantile epileptic encephalopathy 12 2019-12-31 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000515248 SCV000611499 uncertain significance Early infantile epileptic encephalopathy 10; Ataxia-oculomotor apraxia 4 2017-05-23 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000433486 SCV000614683 likely benign not provided 2018-10-24 criteria provided, single submitter clinical testing
Ambry Genetics RCV000716432 SCV000847273 uncertain significance History of neurodevelopmental disorder 2019-02-08 criteria provided, single submitter clinical testing Insufficient evidence
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000515248 SCV000898887 uncertain significance Early infantile epileptic encephalopathy 10; Ataxia-oculomotor apraxia 4 2018-10-24 criteria provided, single submitter clinical testing PNKP NM_007254.3 exon 4 p.Arg139His (c.416G>A): This variant has not been reported in the literature and is present in 0.3% (379/126666) of European alleles, including 2 homozygotes, in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/19-50368466-C-T). This variant is present in ClinVar (Variation ID:159794). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000433486 SCV001151998 uncertain significance not provided 2019-09-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000147358 SCV001288754 likely benign Early infantile epileptic encephalopathy 10 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Division of Human Genetics,Children's Hospital of Philadelphia RCV000147358 SCV000238400 uncertain significance Early infantile epileptic encephalopathy 10 2014-12-12 no assertion criteria provided research The heterozygous variant (c.416G>A; p.Arg139His) in the PNKP gene observed in this patient has not been associated with disease. It occurs at low frequencies in control population (0.2% in ExAC) and a second rare variant was not observed on the other allele. This variant is considered a variant of unknown significance.

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