ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.1880T>A (p.Met627Lys)

dbSNP: rs786204696
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 5
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169507 SCV000220972 pathogenic Autosomal recessive polycystic kidney disease 2014-12-22 criteria provided, single submitter literature only
Invitae RCV000169507 SCV001403649 pathogenic Autosomal recessive polycystic kidney disease 2023-11-13 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with lysine, which is basic and polar, at codon 627 of the PKHD1 protein (p.Met627Lys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with autosomal recessive polycystic kidney disease (PMID: 15805161, 25193386). It is commonly reported in individuals of South African Afrikaner ancestry (PMID: 15805161). ClinVar contains an entry for this variant (Variation ID: 189098). 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. For these reasons, this variant has been classified as Pathogenic.
Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand RCV003398869 SCV004123075 pathogenic Polycystic kidney disease 4 2023-07-01 criteria provided, single submitter research
Laboratory of Gastroenterology and Hepatology, Radboud University Medical Center RCV001844813 SCV001876991 likely pathogenic Autosomal dominant polycystic liver disease 2021-09-01 no assertion criteria provided research
Natera, Inc. RCV000169507 SCV002081058 pathogenic Autosomal recessive polycystic kidney disease 2017-03-16 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.