ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.707+1G>A

gnomAD frequency: 0.00001  dbSNP: rs748365248
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000725728 SCV000338920 pathogenic not provided 2016-02-04 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV001810443 SCV002060235 likely pathogenic Polycystic kidney disease 4 2021-11-11 criteria provided, single submitter clinical testing NM_138694.3(PKHD1):c.707+1G>A is a canonical splice site variant classified as likely pathogenic in the context of autosomal recessive polycystic kidney disease, PKHD1-related. c.707+1G>A has been observed in cases with relevant disease (PMID: 27225849). Functional assessments of this variant are not available in the literature. c.707+1G>A has been observed in population frequency databases (gnomAD: NFE 0.001%). In summary, NM_138694.3(PKHD1):c.707+1G>A is a canonical splice site variant in a gene where loss of function is a known mechanism of disease, is predicted to disrupt protein function, and has been observed more frequently in cases with the relevant disease than in healthy populations.
Invitae RCV000300283 SCV002290151 likely pathogenic Autosomal recessive polycystic kidney disease 2023-01-19 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: 285761). Disruption of this splice site has been observed in individual(s) with polycystic kidney disease (PMID: 27225849). This variant is present in population databases (rs748365248, gnomAD 0.002%). This sequence change affects a donor splice site in intron 10 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).
Fulgent Genetics, Fulgent Genetics RCV001810443 SCV002816571 pathogenic Polycystic kidney disease 4 2022-01-29 criteria provided, single submitter clinical testing
Baylor Genetics RCV001810443 SCV004202208 pathogenic Polycystic kidney disease 4 2023-10-29 criteria provided, single submitter clinical testing

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