ClinVar Miner

Submissions for variant NM_000297.4(PKD2):c.773T>C (p.Leu258Pro)

dbSNP: rs2110104859
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics, University of Goettingen RCV001526880 SCV001737569 likely pathogenic Polycystic kidney disease 2 2021-06-21 criteria provided, single submitter clinical testing The variant c.773T>C (p.(Leu258Pro)) in exon 3 of the PKD2-gene is not found in the gnomAD database and it affects a highly conserved nucleotide a moderately conserved amino acid within a protein domain and there is a moderate physicochemical difference between Leu and Pro. This variant has a pathogenic computational verdict based on 11 pathogenic predictions from BayesDel_addAF, DANN, DEOGEN2, EIGEN, FATHMM-MKL, LIST-S2, M-CAP, MutationAssessor, MutationTaster, PolyPhen-2 and SIFT vs 2 benign predictions from MVP and PrimateAI. This variant was found in an affected individual and his affected mother in our clinic, thus we classify this variant as a likely pathogenic mutation. ACMG criteria used for classification: PM2, PP1, PP2, PP3, PP4.
GeneDx RCV003232373 SCV003929657 uncertain significance not provided 2022-12-02 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; Has not been previously published as pathogenic or benign to our knowledge
Institute of Human Genetics, Cologne University RCV001526880 SCV002035329 uncertain significance Polycystic kidney disease 2 no assertion criteria provided clinical testing

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