Total submissions: 4
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Illumina Laboratory Services, |
RCV001253823 | SCV000451553 | likely benign | Polycystic kidney disease 2 | 2017-04-27 | criteria provided, single submitter | clinical testing | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. |
| Invitae | RCV000269868 | SCV000563112 | benign | Autosomal dominant polycystic kidney disease | 2024-01-18 | criteria provided, single submitter | clinical testing | |
| Gene |
RCV001706567 | SCV001844372 | benign | not provided | 2021-06-22 | criteria provided, single submitter | clinical testing | This variant is associated with the following publications: (PMID: 17100995, 29321346) |
| Department of Pathology and Laboratory Medicine, |
RCV001292296 | SCV001480575 | benign | Polycystic kidney disease | no assertion criteria provided | clinical testing | The PKD2 p.Ile452Val variant was identified in 3 of 758 proband chromosomes (frequency: 0.004) from individuals or families with PKD (Rossetti 2012, Yu 2011, Raj, 2017). The variant was also identified in ClinVar (as Likely benign by 1 submitter, Illumina), and ADPKD Mutation Database (Likely neutral by Athena Diagnostics) databases. The variant was not identified in Genesight-COGR, LOVD 3.0, PKD1-LOVD, databases. The variant was identified in dbSNP (ID: rs1801612) “With Likely benign allele” and in control databases in 592 of 277162 chromosomes at a frequency of 0.002136 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). The variant was identified in the following populations at a frequency greater than 1%: East Asian in 538 of 18868 chromosomes (freq: 0.029). The variant is listed as a polymorphism in both the Chinese Han population (Yu, 2011) and the Korean population (Kim, 1999). In addition, Kim et al. found the variant at a frequency of 0.33 in unaffected controls, and state that the variant is found to be in Hardy-Weinberg equilibrium in the Korean population (Kim 1999). The p.Ile452Val residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. The variant is located with the Polycystin cation channel, PKD1/PKD2 functional domain(s), but both amino acids, wild type and variant, Ile and Val, have hydrophobic side chains. In summary, based on the above information this variant meets our laboratory criteria to be classified as benign. |