ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.3407A>G (p.Tyr1136Cys) (rs41273726)

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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 RCV000153718 SCV000203276 benign not specified 2014-01-21 criteria provided, single submitter clinical testing
Invitae RCV000224414 SCV000218681 benign not provided 2019-03-05 criteria provided, single submitter clinical testing
Counsyl RCV000168029 SCV000220206 likely benign Autosomal recessive polycystic kidney disease 2014-03-30 criteria provided, single submitter literature only
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000224414 SCV000281491 likely benign not provided 2015-02-06 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
PreventionGenetics,PreventionGenetics RCV000153718 SCV000315794 likely benign not specified criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000153718 SCV000592891 likely benign not specified 2016-05-03 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000224414 SCV000699860 likely benign not provided 2017-06-19 criteria provided, single submitter clinical testing Variant summary: The PKHD1 c.3407A>G (p.Tyr1136Cys) variant involves the alteration of a non-conserved nucleotide. 2/4 in silico tools predict a benign outcome for this variant (SNPsandGO not available). This variant was found in 960/121796 control chromosomes (14 homozygotes) at a frequency of 0.007882, which slightly exceeds the estimated maximal expected allele frequency of a pathogenic PKHD1 variant (0.0070711), suggesting this variant is likely a benign polymorphism. In the literature this variant was reported in multiple patients with ARPKD without strong evidence for causality. One reported patient had co-occurrence of a pathogenic variant PKHD1 c. 1458C>A, p.Tyr486X in cis, supporting the non-pathgoenic nature of the variant of interest (Gunay-Aygun_MGM_2010). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as a likely benign.
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000168029 SCV000743915 likely benign Autosomal recessive polycystic kidney disease 2016-12-12 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000168029 SCV000734507 likely benign Autosomal recessive polycystic kidney disease no assertion criteria provided clinical testing

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