ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.7675G>C (p.Val2559Leu) (rs150046042)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000178676 SCV000230801 uncertain significance not provided 2018-03-15 criteria provided, single submitter clinical testing
Blueprint Genetics RCV000178676 SCV000927493 uncertain significance not provided 2017-12-12 criteria provided, single submitter clinical testing
Invitae RCV000806672 SCV000946685 uncertain significance Autosomal recessive polycystic kidney disease 2019-10-10 criteria provided, single submitter clinical testing This sequence change replaces valine with leucine at codon 2559 of the PKHD1 protein (p.Val2559Leu). The valine residue is weakly conserved and there is a small physicochemical difference between valine and leucine. This variant is present in population databases (rs150046042, ExAC 0.2%). This variant has been observed in individuals affected with polycystic kidney disease (PMID: 15805161, 25701400). ClinVar contains an entry for this variant (Variation ID: 197602). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The leucine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Illumina Clinical Services Laboratory,Illumina RCV000806672 SCV001320060 uncertain significance Autosomal recessive polycystic kidney disease 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

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