ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.2961G>T (p.Leu987Phe)

gnomAD frequency: 0.00004  dbSNP: rs398124482
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000082543 SCV000114585 uncertain significance not provided 2013-08-14 criteria provided, single submitter clinical testing
Invitae RCV001243318 SCV001416467 uncertain significance Autosomal recessive polycystic kidney disease 2021-08-30 criteria provided, single submitter clinical testing This sequence change replaces leucine with phenylalanine at codon 987 of the PKHD1 protein (p.Leu987Phe). The leucine residue is moderately conserved and there is a small physicochemical difference between leucine and phenylalanine. 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: 96393). 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 phenylalanine 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 RCV002483154 SCV002790423 uncertain significance Polycystic kidney disease 4 2021-09-13 criteria provided, single submitter clinical testing
Ambry Genetics RCV003242979 SCV003937919 uncertain significance Inborn genetic diseases 2023-05-26 criteria provided, single submitter clinical testing The c.2961G>T (p.L987F) alteration is located in exon 27 (coding exon 26) of the PKHD1 gene. This alteration results from a G to T substitution at nucleotide position 2961, causing the leucine (L) at amino acid position 987 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV001243318 SCV002081008 uncertain significance Autosomal recessive polycystic kidney disease 2018-09-11 no assertion criteria provided clinical testing

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