ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.2027C>G (p.Pro676Arg) (rs115045643)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000082533 SCV000114575 benign not specified 2013-04-15 criteria provided, single submitter clinical testing
Counsyl RCV000169044 SCV000220202 likely benign Autosomal recessive polycystic kidney disease 2014-03-27 criteria provided, single submitter literature only
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000224258 SCV000281335 likely benign not provided 2015-10-29 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Invitae RCV000169044 SCV000291327 benign Autosomal recessive polycystic kidney disease 2019-12-31 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000082533 SCV000315782 benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000082533 SCV000520871 likely benign not specified 2016-09-28 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Integrated Genetics/Laboratory Corporation of America RCV000224258 SCV000699854 likely benign not provided 2016-04-26 criteria provided, single submitter clinical testing Variant summary: Variant affects a non-conserved nucleotide a results in a replacement of a medium size and hydrophobic Proline (P) with a large size and basic Arginine (R). in silico tools predict the variant to be normal; however these predictions have yet to be confirmed by functional studies. The variant was observed predominantly in the African subcohorts of the ExAC project at an allele frequency of 2.3% (including 3 homozygotes) which exceeds ~3 times the maximal expected allele frequency of a disease causing PKHD1 allele (0.7%) indicating the variant to be in the neutral spectrum. The variant was reported in two autosomal-recessive polycystic kidney disease patients in compound heterozygosity with a potentially pathogenic PKHD1 variant. Clinical laboratories classify variant as Benign/Likely benign via ClinVar (without evidence to independently evaluate). Considering all evidence, the variant was classified as Likely Benign.
Mendelics RCV000169044 SCV001137147 benign Autosomal recessive polycystic kidney disease 2019-05-28 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000169044 SCV001325524 likely benign Autosomal recessive polycystic kidney disease 2017-04-28 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. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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