ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.1557C>T (p.Ser519=)

gnomAD frequency: 0.00051  dbSNP: rs142180374
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000147355 SCV000171072 benign not specified 2013-03-21 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.
Genetic Services Laboratory, University of Chicago RCV000147355 SCV000194730 benign not specified 2020-09-21 criteria provided, single submitter clinical testing
Invitae RCV001084690 SCV000560513 benign Developmental and epileptic encephalopathy, 12 2024-01-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV002316394 SCV000850309 benign Inborn genetic diseases 2016-11-10 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Athena Diagnostics Inc RCV000476794 SCV001145119 benign not provided 2018-09-06 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001129139 SCV001288638 benign Microcephaly, seizures, and developmental delay 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.

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