ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.8012G>A (p.Arg2671Gln)

gnomAD frequency: 0.00001  dbSNP: rs778592523
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000588359 SCV000699878 uncertain significance not provided 2016-08-09 criteria provided, single submitter clinical testing Variant summary: The PKHD1 c.8012G>A (p.Arg2671Gln) variant involves the alteration of a non-conserved nucleotide. 4/4 in silico tools predict a benign outcome for this variant. This variant is not located in any known domain (InterPro). This variant is absent in 121358 control chromosomes. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or clinical diagnostic laboratories, nor evaluated for functional impact by in vivo/vitro studies. One internal sample carrying this variant also carries another pathogenic variant (c.3761_3762delCCinsG), however, the phase of the two variants is unknown. Because of the absence of clinical information and the lack of functional studies, the variant is classified as a variant of uncertain significance (VUS) until additional information becomes available.
Invitae RCV001246327 SCV001419671 uncertain significance Autosomal recessive polycystic kidney disease 2021-08-30 criteria provided, single submitter clinical testing This sequence change replaces arginine with glutamine at codon 2671 of the PKHD1 protein (p.Arg2671Gln). The arginine residue is weakly conserved and there is a small physicochemical difference between arginine and glutamine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with PKHD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 496525). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glutamine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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 RCV002506403 SCV002816728 uncertain significance Polycystic kidney disease 4 2021-09-03 criteria provided, single submitter clinical testing
Natera, Inc. RCV001246327 SCV002078000 uncertain significance Autosomal recessive polycystic kidney disease 2018-06-30 no assertion criteria provided clinical testing

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