ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.353del (p.Ser118fs) (rs398124483)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000790659 SCV000231199 pathogenic not provided 2012-10-10 criteria provided, single submitter clinical testing
Counsyl RCV000179010 SCV000678070 likely pathogenic Autosomal recessive polycystic kidney disease 2014-01-02 criteria provided, single submitter clinical testing
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center RCV000179010 SCV000745344 pathogenic Autosomal recessive polycystic kidney disease 2017-03-17 criteria provided, single submitter clinical testing
Invitae RCV000179010 SCV000825136 pathogenic Autosomal recessive polycystic kidney disease 2018-03-16 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser118Ilefs*35) in the PKHD1 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs398124483, ExAC 0.01%). This variant has been reported in several individuals affected with autosomal recessive polycystic kidney disease (PMID: 15108281, 16133180, 15805161). ClinVar contains an entry for this variant (Variation ID: 96397). Loss-of-function variants in PKHD1 are known to be pathogenic (PMID: 19940839). For these reasons, this variant has been classified as Pathogenic.
Illumina Clinical Services Laboratory,Illumina RCV000179010 SCV000915173 likely pathogenic Autosomal recessive polycystic kidney disease 2016-09-28 criteria provided, single submitter clinical testing The PKHD1 c.353delG (p.Ser118IlefsTer35) variant results in a frameshift and is predicted to cause a premature termination of the protein. This variant has been reported in three studies and is found in a total of four individuals with autosomal recessive polycystic kidney disease, including three compound heterozygotes and one heterozygote in whom a second variant could not be identified (Bergmann et al. 2004. Sharp et al. 2005, Losekoot et al. 2005). The p.Ser118IlefsTer35 variant was absent from 300 controls but is reported at a frequency of 0.00013 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the evidence and the potential impact of frameshift variants, the p.Ser118IlefsTer35 variant is classified as likely pathogenic for autosomal recessive polycystic kidney disease. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000179010 SCV000734510 pathogenic Autosomal recessive polycystic kidney disease no assertion criteria provided clinical testing

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