ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.5976_5978del (p.Phe1992_Thr1993delinsLeu)

dbSNP: rs2092438025
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV001280771 SCV001468092 likely pathogenic not provided 2020-09-22 criteria provided, single submitter clinical testing
Athena Diagnostics RCV001280771 SCV001879444 uncertain significance not provided 2021-01-07 criteria provided, single submitter clinical testing
Juno Genomics, Hangzhou Juno Genomics, Inc RCV004796404 SCV005416381 likely pathogenic Polycystic kidney disease, adult type criteria provided, single submitter clinical testing PM4+PM2_Supporting+PS4_Moderate+PP4
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001292029 SCV001481120 uncertain significance Polycystic kidney disease no assertion criteria provided clinical testing The PKD1 p.Phe1992_Thr1993delinsLeu variant was identified in 4 of 2066 proband chromosomes (frequency: 0.002) from individuals or families with ADPKD1 (Audrezet 2012, Rossetti 2001, Rossetti 2007). The variant was also identified in ADPKD Mutation Database (as Highly Likely Pathogenic). The variant was not identified in dbSNP, ClinVar, GeneInsight-COGR, LOVD 3.0, or PKD1-LOVD databases. The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). This variant is an in-frame deletion resulting in the deletion of a phenylalanine (Phe) residue at codon 1992 and a threonine (Thr) residue at codon 1993 as well as the insertion of a single leucine (Leu) residue in their place; the impact of this alteration on PKD1 protein function is not known. This variant has been found to segregate with disease in one family (Audrezet 2012). The variant occurs outside of the splicing consensus sequence and 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predicts 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. This variant is classified as a variant of uncertain significance.

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