ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.1210C>T (p.Arg404Cys)

gnomAD frequency: 0.00001  dbSNP: rs768304312
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 3
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000174762 SCV000226127 uncertain significance not provided 2014-07-21 criteria provided, single submitter clinical testing
Invitae RCV001210502 SCV001381992 uncertain significance Developmental and epileptic encephalopathy, 12 2022-08-09 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 404 of the PNKP protein (p.Arg404Cys). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. 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: 194398). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.
Ambry Genetics RCV002516642 SCV003688928 uncertain significance Inborn genetic diseases 2021-06-11 criteria provided, single submitter clinical testing The c.1210C>T (p.R404C) alteration is located in exon 14 (coding exon 13) of the PNKP gene. This alteration results from a C to T substitution at nucleotide position 1210, causing the arginine (R) at amino acid position 404 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.