ClinVar Miner

Submissions for variant NM_001009944.3(PKD1):c.5957C>T (p.Thr1986Met)

gnomAD frequency: 0.00008  dbSNP: rs200139724
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002708387 SCV003732420 uncertain significance Inborn genetic diseases 2022-03-25 criteria provided, single submitter clinical testing The c.5957C>T (p.T1986M) alteration is located in exon 15 (coding exon 15) of the PKD1 gene. This alteration results from a C to T substitution at nucleotide position 5957, causing the threonine (T) at amino acid position 1986 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV004553944 SCV005043342 uncertain significance Polycystic kidney disease, adult type 2024-02-27 criteria provided, single submitter clinical testing A heterozygous missense variation in exon 15 of the PKD1gene that results in the amino acid substitution of Methionine for Threonine at codon 1986 was detected. The observed variant c.5957C>T (p.Thr1986Met) has a minor allele frequency of 0.0781%, 0.0781% and 0.0155% in the 1000 genomes, Topmed and gnomAD databases. The in silico prediction of the variant is benign by PROVEAN, FATHMM and MutationTaster2 and damaging by SIFT, DANN and LRT. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as a variant of uncertain significance.
Department of Pathology and Laboratory Medicine, Sinai Health System RCV004553944 SCV005919557 uncertain significance Polycystic kidney disease, adult type 2022-04-06 criteria provided, single submitter clinical testing
Genetics laboratory, Department of Obstetrics & Gynae, Institute of Kidney Diseases & Research Centre Dr. H.L. Trivedi Institute Of Transplantation Sciences RCV004553944 SCV005402460 uncertain significance Polycystic kidney disease, adult type 2024-02-27 no assertion criteria provided clinical testing A heterozygous missense variant c.5957C>T (p.Thr1986Met) in exon 15 of PKD1 gene (chr6:2159211; Depth: 110x) was identified. The variant was observed with MAF of 0.07%, 0.07% and 0.02% in the 1000genomes, TopMed and gnomAD databases, respectively. The variant has previously been reported in the ClinVar database as a variant of uncertain significance (RCV002708387). In silico analysis suggests the variant to be damaging by PolyPhen2, SIFT and CADD. Based on the current evidence, the variant is classified as a variant of uncertain significance according to the ACMG-AMP classification system and ClinGen framework.

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