Total submissions: 4
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Athena Diagnostics | RCV000992613 | SCV001145020 | benign | not provided | 2019-05-01 | criteria provided, single submitter | clinical testing | |
| ARUP Laboratories, |
RCV001001926 | SCV001159690 | benign | Polycystic kidney disease, adult type | 2019-01-07 | criteria provided, single submitter | clinical testing | |
| Gene |
RCV000992613 | SCV001910065 | benign | not provided | 2021-02-25 | criteria provided, single submitter | clinical testing | This variant is associated with the following publications: (PMID: 11316854, 22185115) |
| Department of Pathology and Laboratory Medicine, |
RCV001292269 | SCV001480928 | likely benign | Polycystic kidney disease | no assertion criteria provided | clinical testing | The PKD1 p.Gly3052Gly variant was identified in 1 of 82 proband chromosomes (frequency: 0.01) from individuals or families with ADPKD of Thai ethnicity, and was not identified in 100 control chromosomes from healthy individuals (Phakdeekitcharoen 2001). The variant was identified in dbSNP (ID: rs371368338) as “NA”, in the ADPKD Mutation Database 3x as likely neutral, in the 1000 Genomes Project in 27 of 5000 chromosomes (frequency: 0.005), in the Exome Aggregation Consortium database (August 8, 2016) in 20 of 19184 chromosomes (frequency: 0.001) in the following populations: East Asian in 16 of 638 chromosomes (frequency: 0.03), European (Non-Finnish) in 2 of 7156 chromosomes (frequency: 0.0003), South Asian in 2 of 7982 chromosomes (frequency: 0.0003), but was not seen in the African, Finnish and Latino populations. The variant was not identified in the Clinvitae, ClinVar, GeneInsight-COGR, MutDB, PKD1-LOVD, and PKD1-LOVD 3.0 databases or the NHLBI GO Exome Sequencing Project. In addition the variant was identified by our laboratory as co-occurring along with a pathogenic variant (PKD1, EXON 15, c.3346C>T, p.Gln1116X) in an individuals with PKD suggesting that the variant may not have clinical significance. The p.Gly3052Gly variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. However 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. |