ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.1397G>A (p.Gly466Glu)

dbSNP: rs750730042
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 7
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000671679 SCV000796678 likely pathogenic Autosomal recessive polycystic kidney disease 2017-12-21 criteria provided, single submitter clinical testing
Invitae RCV000671679 SCV001387436 pathogenic Autosomal recessive polycystic kidney disease 2023-07-25 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Gly466 amino acid residue in PKHD1. Other variant(s) that disrupt this residue have been observed in individuals with PKHD1-related conditions (PMID: 28933340, 29520754), which suggests that this may be a clinically significant amino acid residue. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PKHD1 protein function. ClinVar contains an entry for this variant (Variation ID: 555789). This missense change has been observed in individual(s) with autosomal recessive polycystic kidney disease (PMID: 20413436, 27225849, 27752906). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (no rsID available, gnomAD 0.002%). This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 466 of the PKHD1 protein (p.Gly466Glu).
Revvity Omics, Revvity RCV001784272 SCV002024652 likely pathogenic Polycystic kidney disease 4 2021-02-10 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001784272 SCV002801684 pathogenic Polycystic kidney disease 4 2022-04-14 criteria provided, single submitter clinical testing
GeneDx RCV002509503 SCV002819040 likely pathogenic not provided 2023-01-05 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27225849, 19914852)
Baylor Genetics RCV001784272 SCV004204727 pathogenic Polycystic kidney disease 4 2023-02-15 criteria provided, single submitter clinical testing
Natera, Inc. RCV000671679 SCV002081083 pathogenic Autosomal recessive polycystic kidney disease 2021-04-21 no assertion criteria provided clinical testing

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.