ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.4654G>A (p.Val1552Ile)

gnomAD frequency: 0.00121  dbSNP: rs149874529
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000712624 SCV000843141 benign not provided 2017-11-01 criteria provided, single submitter clinical testing
GeneDx RCV000712624 SCV001982924 uncertain significance not provided 2024-04-05 criteria provided, single submitter clinical testing In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004768605 SCV005381556 likely benign not specified 2024-08-28 criteria provided, single submitter clinical testing Variant summary: PKD1 c.4654G>A (p.Val1552Ile) results in a conservative amino acid change located in the PKD domain (IPR000601) of the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00022 in 248018 control chromosomes, predominantly at a frequency of 0.0025 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 5 fold of the estimated maximal expected allele frequency for a pathogenic variant in PKD1 causing Polycystic Kidney Disease 1 phenotype (0.0005). To our knowledge, no occurrence of c.4654G>A in individuals affected with Polycystic Kidney Disease 1 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 586277). Based on the evidence outlined above, the variant was classified as likely benign.
PreventionGenetics, part of Exact Sciences RCV003928181 SCV004740970 likely benign PKD1-related disorder 2020-12-08 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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