ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.6779A>G (p.Tyr2260Cys)

gnomAD frequency: 0.00006  dbSNP: rs374132086
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000730602 SCV000858350 uncertain significance not provided 2017-11-22 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001165236 SCV001327413 uncertain significance Autosomal recessive polycystic kidney disease 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Fulgent Genetics, Fulgent Genetics RCV002493327 SCV002799531 uncertain significance Polycystic kidney disease 4 2022-03-02 criteria provided, single submitter clinical testing
Invitae RCV001165236 SCV003274385 uncertain significance Autosomal recessive polycystic kidney disease 2022-08-16 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 2260 of the PKHD1 protein (p.Tyr2260Cys). This variant is present in population databases (rs374132086, gnomAD 0.1%). This missense change has been observed in individual(s) with clinical features of polycystic kidney disease (PMID: 25771912). ClinVar contains an entry for this variant (Variation ID: 595136). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PKHD1 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.

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