Submissions for variant NM_007254.4(PNKP):c.58C>T (p.Pro20Ser)

gnomAD frequency: 0.00946  dbSNP: rs3739168

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000081512	SCV000113443	benign	not specified	2013-09-06	criteria provided, single submitter	clinical testing
GeneDx	RCV000230285	SCV000171074	benign	not provided	2018-11-08	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 27470939, 23708187, 26993267, 25728773, 27125728)
Genetic Services Laboratory, University of Chicago	RCV000081512	SCV000194740	benign	not specified	2013-07-30	criteria provided, single submitter	clinical testing
Invitae	RCV001081799	SCV000289711	benign	Developmental and epileptic encephalopathy, 12	2024-02-01	criteria provided, single submitter	clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000081512	SCV000540071	likely benign	not specified	2016-06-02	criteria provided, single submitter	clinical testing	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: reported in 1 homozygous individual with epileptic encephalopathy by Carvill, 2013. However, the frequency in ExAC (0.75% in ExAC) and the presence of 5 homozygotes in ExAC argue against a pathogenic role for this variant
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000625160	SCV000743938	benign	Microcephaly, seizures, and developmental delay	2014-10-09	criteria provided, single submitter	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000625160	SCV000745400	benign	Microcephaly, seizures, and developmental delay	2017-05-31	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002311645	SCV000846973	benign	Inborn genetic diseases	2017-05-24	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.
Mendelics	RCV000230285	SCV001135140	benign	not provided	2019-05-28	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000625160	SCV001291586	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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
CeGaT Center for Human Genetics Tuebingen	RCV000230285	SCV002543964	benign	not provided	2024-02-01	criteria provided, single submitter	clinical testing	PNKP: BS1, BS2