ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.8581A>G (p.Ser2861Gly) (rs150925674)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000197457 SCV000252884 benign Autosomal recessive polycystic kidney disease 2019-12-31 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000254142 SCV000315845 likely benign not specified criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000254142 SCV000331145 benign not specified 2015-10-28 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590788 SCV000699882 benign not provided 2017-08-21 criteria provided, single submitter clinical testing Variant summary: The PKHD1 c.8581A>G (p.Ser2861Gly) variant involves the alteration of a non-conserved nucleotide and 2/3 in silico tools (SNPsandGO and Mutation Taster not captured due to low reliability index and p-value, respectively) predict a benign outcome for this variant. This variant was found in 1011/276778 control chromosomes, predominantly observed in the European (Finnish) subpopulation at a frequency of 0.019838 (509/25658). This frequency is about 3 times the estimated maximal expected allele frequency of a pathogenic PKHD1 variant (0.0070711), suggesting this is likely a benign polymorphism found primarily in the populations of European (Finnish) origin. The variant of interest has been reported in multiple affected individuals including individuals that were compound heterozygotes for two pathogenic variants, further supporting the variant of interest being in the benign spectrum. The reports of its occurence in cis with another pathogenic variant in patients with a confirmed second disease causing variation, provides further supporting evidence in favor of its benign outcome. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as "likely benign/benign." Taken together, this variant is classified as Benign.
SIB Swiss Institute of Bioinformatics RCV000197457 SCV000803596 likely benign Autosomal recessive polycystic kidney disease 2018-05-31 criteria provided, single submitter curation This variant is interpreted as a Likely Benign, for Polycystic kidney disease 4 with or without polycystic liver disease, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: BP4 => Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.). BS2 => Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
Mendelics RCV000197457 SCV001137139 benign Autosomal recessive polycystic kidney disease 2019-05-28 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000197457 SCV001323390 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.

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