Total submissions: 8
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Center for Pediatric Genomic Medicine, |
RCV000440845 | SCV000511619 | pathogenic | not provided | 2017-01-06 | criteria provided, single submitter | clinical testing | |
Blueprint Genetics | RCV000440845 | SCV000927917 | likely pathogenic | not provided | 2018-09-05 | criteria provided, single submitter | clinical testing | |
Baylor Genetics | RCV001004198 | SCV001163037 | pathogenic | Autosomal recessive polycystic kidney disease | criteria provided, single submitter | clinical testing | ||
Hudson |
RCV001775118 | SCV002012479 | likely pathogenic | Polycystic kidney disease 4 | 2014-10-13 | criteria provided, single submitter | research | ACMG codes: PM2; PM3; PP3; PP5 |
Gene |
RCV000440845 | SCV002030916 | likely pathogenic | not provided | 2023-01-17 | 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: 31589614, 25263802, 14741187, 12874454, 22034641, 15805161) |
Invitae | RCV001004198 | SCV002208061 | pathogenic | Autosomal recessive polycystic kidney disease | 2024-01-17 | criteria provided, single submitter | clinical testing | This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 1971 of the PKHD1 protein (p.Gly1971Asp). This variant is present in population databases (rs180675584, gnomAD 0.009%). This missense change has been observed in individuals with polycystic kidney disease (PMID: 12874454, 19940839). ClinVar contains an entry for this variant (Variation ID: 377269). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PKHD1 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic. |
Baylor Genetics | RCV001775118 | SCV004204618 | pathogenic | Polycystic kidney disease 4 | 2023-07-02 | criteria provided, single submitter | clinical testing | |
Sydney Genome Diagnostics, |
RCV001004198 | SCV001449399 | likely pathogenic | Autosomal recessive polycystic kidney disease | 2018-05-22 | no assertion criteria provided | clinical testing | This individual is heterozygous for the c.5912G>A variant in the PKHD1 gene. This variant has been previously reported in patients with autosomal recessive polycystic kidney disease either in the homozygous form or compound heterozygous with a second pathogenic PKHD1 variant (Sharp et al J Med Genet 2005; 42:336-349; Bergmann et al 2011 J Am Soc Nephrol 22: 2047-2056). This variant has been reported in the gnomAD browser (http://gnomad.broadinstitute.org) with a low allele frequency of 0.004% (12/ 276, 768 alleles). In silico analysis of pathogenicity (through Alamut Visual v2.8.1) using PolyPhen2, SIFT and MutationTaster suggest that this variant is likely to be pathogenic. This variant is considered to be likely pathogenic according to the ACMG guidelines. |