ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.1397G>A (p.Gly466Glu) (rs750730042)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000671679 SCV000796678 likely pathogenic Autosomal recessive polycystic kidney disease 2017-12-21 criteria provided, single submitter clinical testing
Invitae RCV000671679 SCV001387436 likely pathogenic Autosomal recessive polycystic kidney disease 2019-06-19 criteria provided, single submitter clinical testing This sequence change replaces glycine with glutamic acid at codon 466 of the PKHD1 protein (p.Gly466Glu). The glycine residue is moderately conserved and there is a moderate physicochemical difference between glycine and glutamic acid. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individuals affected with polycystic kidney disease (PMID: 20413436, 27225849, 27752906). ClinVar contains an entry for this variant (Variation ID: 555789). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant disrupts the p.Gly466 amino acid residue in PKHD1. Other variant(s) that disrupt this residue have been observed in individuals with PKHD1-related conditions (PMID: 15698423, 29520754), which suggests that this may be a clinically significant amino acid residue. 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.

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