ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.3367G>A (p.Gly1123Ser) (rs142107837)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169334 SCV000220676 likely pathogenic Autosomal recessive polycystic kidney disease 2014-09-08 criteria provided, single submitter literature only
Invitae RCV000169334 SCV000629914 likely pathogenic Autosomal recessive polycystic kidney disease 2018-08-09 criteria provided, single submitter clinical testing This sequence change replaces glycine with serine at codon 1123 of the PKHD1 protein (p.Gly1123Ser). The glycine residue is moderately conserved and there is a small physicochemical difference between glycine and serine. This variant is present in population databases (rs142107837, ExAC 0.001%). This variant has been observed on the opposite chromosome (in trans) from several different variants, including at least one loss-of-function variant, in individuals affected with autosomal recessive polycystic kidney disease (PMID: 12506140, 12874454, 15698423, 15805161). Individuals homozygous for this variant have also been described, generally with later onset of disease than other reported individuals (PMID: 15805161, 25966130). ClinVar contains an entry for this variant (Variation ID: 188959). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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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