ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.1462C>T (p.Arg488Trp)

gnomAD frequency: 0.00003  dbSNP: rs139770251
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000796883 SCV000936416 uncertain significance Autosomal recessive polycystic kidney disease 2021-08-24 criteria provided, single submitter clinical testing This sequence change replaces arginine with tryptophan at codon 488 of the PKHD1 protein (p.Arg488Trp). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is present in population databases (rs139770251, ExAC 0.001%). This variant has not been reported in the literature in individuals affected with PKHD1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Fulgent Genetics, Fulgent Genetics RCV002501054 SCV002787426 uncertain significance Polycystic kidney disease 4 2021-12-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV003166146 SCV003863674 uncertain significance Inborn genetic diseases 2023-01-26 criteria provided, single submitter clinical testing The c.1462C>T (p.R488W) alteration is located in exon 16 (coding exon 15) of the PKHD1 gene. This alteration results from a C to T substitution at nucleotide position 1462, causing the arginine (R) at amino acid position 488 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV000796883 SCV002081078 uncertain significance Autosomal recessive polycystic kidney disease 2018-10-09 no assertion criteria provided clinical testing

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