ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.881-1G>A

dbSNP: rs1554220431
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000726993 SCV000704791 pathogenic not provided 2016-12-20 criteria provided, single submitter clinical testing
Counsyl RCV000594446 SCV000790433 likely pathogenic Autosomal recessive polycystic kidney disease 2017-05-02 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000594446 SCV001574616 likely pathogenic Autosomal recessive polycystic kidney disease 2023-01-20 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: 499351). Disruption of this splice site has been observed in individual(s) with polycystic kidney disease (PMID: 15805161). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 12 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).
Genome-Nilou Lab RCV001580522 SCV001810577 pathogenic Polycystic kidney disease 4 2021-07-22 criteria provided, single submitter clinical testing
GeneDx RCV000726993 SCV002820356 likely pathogenic not provided 2022-07-15 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: 25525159, 15805161)
Baylor Genetics RCV001580522 SCV004204623 pathogenic Polycystic kidney disease 4 2023-06-26 criteria provided, single submitter clinical testing

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