ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.9553G>A (p.Val3185Ile)

gnomAD frequency: 0.00066  dbSNP: rs145651593
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001087159 SCV000629937 likely benign Autosomal recessive polycystic kidney disease 2024-01-22 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000592975 SCV000702120 uncertain significance not provided 2017-11-22 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000780599 SCV000918007 uncertain significance not specified 2017-12-11 criteria provided, single submitter clinical testing Variant summary: The c.9553G>A (p.Val3185Ile) in PKHD1 gene is a missense variant involves a non-conserved nucleotide located outside of any known functional domain or repeat. The 4/4 in silico tools used predict benign outcome for this variant, however no functional studies supporting these predictions were published at the time of evaluation. The c. 9553G>A was identified in the control population dataset of gnomAD at a low frequency of 0.00024 (69/276536 chrs tested), predominantly in individuals of African descent (0.0027; 64/24022 chrs). The observed frequencies do not exceed the maximum expected allele frequency for a pathogenic variant of 0.007, suggesting that it is not a common polymorphism. To our knowledge, the variant has not been reported in affected individuals via peer-reviewed reports or cited by reputable databases/clinical laboratories. Taken together, the variant was classified as VUS, until new information becomes available.
Mayo Clinic Laboratories, Mayo Clinic RCV000592975 SCV002542178 uncertain significance not provided 2022-03-14 criteria provided, single submitter clinical testing BP4
Ambry Genetics RCV002527687 SCV003717429 uncertain significance Inborn genetic diseases 2021-11-12 criteria provided, single submitter clinical testing The c.9553G>A (p.V3185I) alteration is located in exon 58 (coding exon 57) of the PKHD1 gene. This alteration results from a G to A substitution at nucleotide position 9553, causing the valine (V) at amino acid position 3185 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV003962477 SCV004791316 likely benign PKHD1-related disorder 2022-12-12 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. RCV001087159 SCV001455237 uncertain significance Autosomal recessive polycystic kidney disease 2018-04-17 no assertion criteria provided clinical testing

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