ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.3679G>T (p.Ala1227Ser) (rs150710956)

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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 Inc RCV000992576 SCV001144976 benign not specified 2020-09-04 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001000819 SCV001157884 likely benign Polycystic kidney disease, adult type 2019-01-22 criteria provided, single submitter clinical testing
Molecular Genetics of Inherited Kidney Disorders Laboratory,Garvan Institute of Medical Research RCV001254279 SCV001430244 likely benign Autosomal dominant polycystic kidney disease 2019-01-01 criteria provided, single submitter research
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001357786 SCV001553363 uncertain significance not provided no assertion criteria provided clinical testing The PKD1 p.Ala1227Ser variant was not identified in the literature nor was it identified in the ClinVar or LOVD 3.0. The variant was identified in dbSNP (ID: rs150710956) and the ADPKD Mutation Database (predicted likely neutral). The variant was also identified in control databases in 168 of 270900 chromosomes at a frequency of 0.00062 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Other in 8 of 6962 chromosomes (freq: 0.001149), European (Finnish) in 27 of 23832 chromosomes (freq: 0.001133), European (non-Finnish) in 118 of 122276 chromosomes (freq: 0.000965), Latino in 13 of 34970 chromosomes (freq: 0.000372) and African in 2 of 23170 chromosomes (freq: 0.000086); it was not observed in the Ashkenazi Jewish, East Asian, and 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.Ala1227 residue is conserved in mammals but not in more distantly related organisms however computational analyses (SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict 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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