ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.3489C>T (p.Phe1163=)

gnomAD frequency: 0.01269  dbSNP: rs139744826
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
PreventionGenetics, part of Exact Sciences RCV000251408 SCV000305727 benign not specified criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000992574 SCV001144974 benign not provided 2018-10-16 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001001962 SCV001159760 benign Polycystic kidney disease, adult type 2018-09-04 criteria provided, single submitter clinical testing
GeneDx RCV000992574 SCV001886914 benign not provided 2020-04-30 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001292080 SCV001480820 benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Phe1163Phe variant was identified in 1 of 164 proband chromosomes (frequency: 0.006) from individuals or families with ADPKD (Garcia-Gonzalez 2007), ClinVar and Clinvitae (as Benign by Prevention Genetics), ADPKD Mutation Database (Likely neutral), GeneInsight-COGR (as Benign by a clinical laboratory). The variant was identified in dbSNP (ID: rs139744826) as “With Benign allele”, with a minor allele frequency of 0.01 (58 of 5000 chromosomes in 1000 Genomes Project), the NHLBI GO Exome Sequencing Project in 4 of 8468 European American (frequency: 0.0005) and in 161 of 4280 African American alleles (frequency: 0.04), the Exome Aggregation Consortium database (August 8, 2016) in 228 (3 homozygous) of 30390 chromosomes (frequency: 0.008) in the following populations: African in 191 of 3092 chromosomes (frequency:0.06), Latino in 12 of 1416 chromosomes (frequency: 0.008), European (Non-Finnish) in 22 of 14238 chromosomes (frequency: 0.002), South Asian in 1 of 9058 chromosomes (frequency: 0.0001), and in Other in 2 of 264 chromosomes (frequency: 0.008)and was not identified in East Asian and Finnish populations, increasing the likelihood this could be a low frequency benign variant. In addition we cannot be certain that data from control databases is specific to PKD1 and not from one of the six PKD1 pseudogenes. The variant was identified by our laboratory in 1 individual with ADPKD, co-occurring with a pathogenic PKD1 variant (c.12178C>T, p.Gln4060X), increasing the likelihood that the variant does not have clinical significance. The p.Phe1163Phe variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, and HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, this variant meets our laboratory criteria to be classified as benign.

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.