ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.4632G>A (p.Val1544=)

gnomAD frequency: 0.00004  dbSNP: rs142035983
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Fulgent Genetics, Fulgent Genetics RCV002493531 SCV002791727 uncertain significance Polycystic kidney disease, adult type 2022-05-06 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001292168 SCV001480793 uncertain significance Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Val1544= variant was not identified in the literature nor was it identified in the ClinVar, LOVD 3.0, ADPKD Mutation Database or the PKD1-LOVD databases. The variant was identified in dbSNP (ID: rs142035983) as "NA”. It was also identified in control databases in 9 of 275030 chromosomes at a frequency of 0.00003 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the African population in 9 of 23758 chromosomes (freq: 0.0004), while it was not observed in the Other, Latino, European, Ashkenazi Jewish, East Asian, Finnish or South Asian populations. 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.Val1544= 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, 3 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; this information is not predictive enough to assume pathogenicity. This variant was identified by our laboratory as co-occurring with a pathogenic PKD1 variant (c.3356dup, p.Val1120Cysfs*16), increasing the likelihood that the p.Val1544= variant does not have clinical significance. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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