ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.5909-2del

dbSNP: rs1334913120
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000666217 SCV000790474 likely pathogenic Autosomal recessive polycystic kidney disease 2017-03-24 criteria provided, single submitter clinical testing
GeneDx RCV003156279 SCV003845595 likely pathogenic not provided 2023-03-26 criteria provided, single submitter clinical testing Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25114813)
PreventionGenetics, part of Exact Sciences RCV003411573 SCV004115410 pathogenic PKHD1-related disorder 2023-08-11 criteria provided, single submitter clinical testing The PKHD1 c.5909-2delA variant is predicted to result in a deletion affecting a canonical splice site. This variant has been reported to be pathogenic for autosomal recessive polycystic kidney disease (ARPKD) (Thakur et al. 2014. PubMed ID: 25114813). To our knowledge, this variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. In ClinVar, this variant has been interpreted as likely pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/551218/). This variant is interpreted as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV000666217 SCV004293754 likely pathogenic Autosomal recessive polycystic kidney disease 2023-09-27 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 551218). Disruption of this splice site has been observed in individual(s) with autosomal recessive polycystic kidney disease (PMID: 25114813). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a splice site in intron 36 of the PKHD1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PKHD1 are known to be pathogenic (PMID: 19940839).
Baylor Genetics RCV004568498 SCV005056318 pathogenic Polycystic kidney disease 4 2024-02-15 criteria provided, single submitter clinical testing

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