ClinVar Miner

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

gnomAD frequency: 0.00003  dbSNP: rs142107837
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Total submissions: 6
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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
Labcorp Genetics (formerly Invitae), Labcorp RCV000169334 SCV000629914 pathogenic Autosomal recessive polycystic kidney disease 2023-10-07 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 1123 of the PKHD1 protein (p.Gly1123Ser). This variant is present in population databases (rs142107837, gnomAD 0.002%). This missense change has been observed in individual(s) with autosomal recessive polycystic kidney disease (PMID: 12506140, 12874454, 15698423, 15805161, 25966130; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 188959). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001843489 SCV002102769 pathogenic not provided 2022-03-02 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24984783, 31589614, 25966130, 15805161, 12874454, 12506140, 15698423)
Fulgent Genetics, Fulgent Genetics RCV002492692 SCV002776281 pathogenic Polycystic kidney disease 4 2024-01-23 criteria provided, single submitter clinical testing
Baylor Genetics RCV002492692 SCV004204580 pathogenic Polycystic kidney disease 4 2024-03-13 criteria provided, single submitter clinical testing
Natera, Inc. RCV000169334 SCV002080999 pathogenic Autosomal recessive polycystic kidney disease 2017-08-31 no assertion criteria provided clinical testing

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