ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.3467C>T (p.Ser1156Leu) (rs367707903)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Blueprint Genetics RCV000788447 SCV000927563 likely pathogenic not provided 2018-03-04 criteria provided, single submitter clinical testing
Baylor Genetics RCV001004206 SCV001163051 likely pathogenic Autosomal recessive polycystic kidney disease criteria provided, single submitter clinical testing
Invitae RCV001004206 SCV001198042 likely pathogenic Autosomal recessive polycystic kidney disease 2019-12-14 criteria provided, single submitter clinical testing This sequence change replaces serine with leucine at codon 1156 of the PKHD1 protein (p.Ser1156Leu). The serine residue is weakly conserved and there is a large physicochemical difference between serine and leucine. This variant is present in population databases (rs367707903, ExAC 0.006%). This variant has been observed in individual(s) with autosomal recessive polycystic kidney disease (PMID: 16199545, 27225849, 20413436). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 636580). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
Natera Inc RCV001027935 SCV001190665 likely pathogenic Polycystic kidney disease 2019-05-20 no assertion criteria provided clinical testing

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