ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.6777C>T (p.Phe2259=) (rs140065359)

Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 4
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000153712 SCV000203270 benign not specified 2014-01-17 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000336710 SCV000464072 uncertain significance Autosomal recessive polycystic kidney disease 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000153712 SCV000918003 benign not specified 2017-12-21 criteria provided, single submitter clinical testing Variant summary: The PKHD1 c.6777C>T (p.Phe2259Phe) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE site of SC35. However, these predictions have yet to be confirmed by functional studies. This variant was found in 1516/276908 control chromosomes (12 homozygotes), predominantly observed in the European (Finnish) subpopulation at a frequency of 0.014629 (377/25770). This frequency is about 2 times the estimated maximal expected allele frequency of a pathogenic PKHD1 variant (0.0070711), suggesting this is likely a benign polymorphism found primarily in the populations of European (Finnish) origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, by applying ACMG rules (BS1, BS2, BP6, BP7) this variant is classified as benign.
Invitae RCV000336710 SCV000557639 benign Autosomal recessive polycystic kidney disease 2017-11-14 criteria provided, single submitter 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.