ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.730G>C (p.Gly244Arg)

gnomAD frequency: 0.00013  dbSNP: rs562480894
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000420129 SCV000511571 uncertain significance not provided 2016-09-13 criteria provided, single submitter clinical testing Converted during submission to Uncertain significance.
GeneDx RCV000420129 SCV000572594 uncertain significance not provided 2017-08-31 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the PNKP gene.The G244R variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The G244R variant is observed in 7/9874 (0.07%) alleles from individuals of African background, including one homozygous individual (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The G244R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals, and in silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV000815582 SCV000956043 likely benign Developmental and epileptic encephalopathy, 12 2023-11-19 criteria provided, single submitter clinical testing
Ambry Genetics RCV002379288 SCV002671019 uncertain significance Inborn genetic diseases 2018-04-24 criteria provided, single submitter clinical testing The p.G244R variant (also known as c.730G>C), located in coding exon 6 of the PNKP gene, results from a G to C substitution at nucleotide position 730. The glycine at codon 244 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV000420129 SCV004236198 uncertain significance not provided 2023-04-17 criteria provided, single submitter clinical testing

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