ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.4495C>T (p.Leu1499=) (rs142002333)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000250082 SCV000305741 likely benign not specified criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001286710 SCV001473322 benign Polycystic kidney disease, adult type 2020-06-02 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000250082 SCV001476609 benign not specified 2019-11-19 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001292095 SCV001480885 likely benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Leu1499= variant was identified in 5 of 578 proband chromosomes (frequency: 0.009) from individuals or families with ADPKD (Rossetti 2012, Tan 2009). The variant was also identified in the following databases: dbSNP (ID: rs142002333) as “with Likely benign allele”, ClinVar (classified as likely benign by Prevention Genetics), GeneInsight-COGR (classified as benign by a clinical laboratory - LMM), ADPKD Mutation Database (classified as likely neutral). The variant was not identified in LOVD 3.0, PKD1-LOVD, databases. The variant was identified in control databases in 713 (1 homozygous) of 274464 chromosomes at a frequency of 0.003 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). In addition we cannot be certain that data from control databases is specific to PKD1 and not from one of the six PKD1 pseudogenes. The p.Leu1499= 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. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. 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.

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