ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.3183G>A (p.Glu1061=) (rs148727945)

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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 RCV000245641 SCV000305720 likely benign not specified criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000992573 SCV001144972 benign not provided 2019-01-24 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001285327 SCV001471740 likely benign Polycystic kidney disease, adult type 2020-02-26 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001291870 SCV000592757 benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Glu1061Glu variant was identified in 1 of 164 proband chromosomes (frequency: 0.006) from individuals or families with clinical features of polycystic renal disease (Garcia-Gonzalez 2007). The variant was also identified in dbSNP (ID: rs148727945) as “NA”, in the ADPKD Mutation Database (classification “likely neutral”), but was not in Clinvitae, ClinVar , GeneInsight COGR, PKD1-LOVD, and PKD1-LOVD 3.0. This variant was identified in the 1000 Genomes Project in 5 of 5000 chromosomes (frequency: 0.001), HAPMAP-EUR in 5 of 1006 chromosomes (frequency: 0.005), NHLBI GO Exome Sequencing Project in 10 of 4570 European American alleles and in 2 of 2590 African American alleles, and in the Exome Aggregation Consortium database (March 14, 2016) in 84 of 43768 alleles, specifically in 68 of 22746 alleles (1 homozygous, frequency: 0.0030) from a population of European (Non-Finnish) individuals, in 14 of 3386 alleles (frequency: 0.0041) from a Latino population, and in 2 of 2432 alleles (frequency: 0.0008) from an African population. The variant was not seen in East Asian, South Asian, or European (Finnish) populations. The p.Glu1061Glu 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. This variant was identified in our laboratory in one individual with ADPKD and a co-occurring pathogenic variant in PKD1 (c.160_166dup, p.Leu56ProfsX60), increasing the likelihood this variant does not have clinical significance. In summary, based on the above information, this variant meets our laboratory criteria to be classified as benign.

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