ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.3006G>C (p.Val1002=)

gnomAD frequency: 0.00239  dbSNP: rs143013095
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001658189 SCV001872706 likely benign not provided 2021-03-12 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002500870 SCV002811390 likely benign Polycystic kidney disease, adult type 2021-10-25 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001658189 SCV004142900 likely benign not provided 2024-01-01 criteria provided, single submitter clinical testing PKD1: BP4, BP7
PreventionGenetics, part of Exact Sciences RCV003891867 SCV000305715 benign PKD1-related disorder 2020-07-12 no assertion criteria provided clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001291869 SCV000592754 likely benign Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 c.3006G>C variant was not identified in the literature nor was it identified in the Clinvitae, ClinVar, GeneInsight COGR, MutDB, PKD1-LOVD, and PKD1-LOVD 3.0 databases. The variant was identified in dbSNP (ID: rs143013095) as “N/A”, and the ADPKD Mutation Database (classified as likely neutral by Athena Diagnostics). This variant was also identified in the 1000 Genomes Project in 2 of 5000 chromosomes (frequency: 0.0004), NHLBI GO Exome Sequencing Project in 8 of 8600 European American alleles, the Exome Aggregation Consortium database (August 8, 2016) in 136 of 119208 chromosomes (freq. 0.001) in the following populations: European in 122 of 65136 chromosomes (freq. 0.002), Finnish in 11 of 6556 chromosomes (freq. 0.002), Latino in 2 of 11502 chromosomes (freq. 0.0002) and Other in 1 of 880 chromosomes (freq. 0.001), although this low number of observations and low frequency is not substantive enough to determine the prevalence of the variant in the general population and its relationship to disease. The p.Val1002Val 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. The variant occurs outside of the splicing consensus sequence and 3 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume 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.

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