ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.1675C>T (p.Arg559Trp)

gnomAD frequency: 0.00055  dbSNP: rs141384205
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586006 SCV000699851 benign not provided 2016-06-12 criteria provided, single submitter clinical testing Variant summary: The PKHD1 c.1675C>T (p.Arg559Trp) variant involves the alteration of a non-conserved nucleotide. 3/4 in silico tools predict a benign outcome (SNPs&GO not captured due to low reliability index). This variant was found in 221/123690 control chromosomes (including 5 homozygotes), predominantly observed in the East Asian subpopulation at a frequency of 0.0201716 (174/8626). This frequency is about 3 times greater than 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 East Asian. In a sufficiently large case-control study, this variant did not confer any increased risk for non-obstructive azoospermia, further supporting the benign outcome. Taking together, the variant is classified as Benign.
Invitae RCV001083536 SCV001002827 benign Autosomal recessive polycystic kidney disease 2024-01-31 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001083536 SCV001320522 benign 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). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.
Natera, Inc. RCV001083536 SCV002081070 benign Autosomal recessive polycystic kidney disease 2017-05-11 no assertion criteria provided clinical testing

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