ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.171A>G (p.Gln57=)

gnomAD frequency: 0.00006  dbSNP: rs543640706
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001496254 SCV001700950 likely benign Autosomal recessive polycystic kidney disease 2023-11-25 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003973190 SCV004794918 likely benign PKHD1-related disorder 2021-09-14 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).
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001292017 SCV001481092 uncertain significance Polycystic kidney disease no assertion criteria provided clinical testing The PKHD1 p.Gln57= variant was not identified in the literature nor was it identified in the ClinVar, LOVD 3.0, or the RWTH AAachen University ARPKD database. The variant was identified in the dbSNP database (ID: rs543640706) and in control databases in 15 of 246170 chromosomes at a frequency of 0.00006 (Genome Aggregation Database Feb 27, 2017). Breakdown of the observations by population include Latino in 1 of 33576 chromosomes (freq: 0.00003) and South Asian in 14 of 30782 chromosomes (freq: 0.0005). The variant was not observed in the African, Other, European, Ashkenazi Jewish, East Asian, or Finnish populations. The p.Gln57= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. However, 3 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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