ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.9493G>A (p.Val3165Met)

gnomAD frequency: 0.00025  dbSNP: rs199621305
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000281542 SCV000464042 uncertain significance Autosomal recessive polycystic kidney disease 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Eurofins Ntd Llc (ga) RCV000592543 SCV000704006 uncertain significance not provided 2016-11-23 criteria provided, single submitter clinical testing
Invitae RCV000281542 SCV001004854 benign Autosomal recessive polycystic kidney disease 2024-01-28 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000592543 SCV001154768 uncertain significance not provided 2018-06-01 criteria provided, single submitter clinical testing
GeneDx RCV000592543 SCV002569894 uncertain significance not provided 2022-03-02 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
PreventionGenetics, part of Exact Sciences RCV003902391 SCV004721277 likely benign PKHD1-related condition 2023-01-24 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV000281542 SCV001455238 benign Autosomal recessive polycystic kidney disease 2020-01-03 no assertion criteria provided clinical testing

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