ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.5750A>G (p.Gln1917Arg)

gnomAD frequency: 0.00004  dbSNP: rs1412045164
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001004200 SCV001163040 likely pathogenic Autosomal recessive polycystic kidney disease criteria provided, single submitter clinical testing
GeneDx RCV001786423 SCV002028864 likely pathogenic not provided 2023-01-20 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 12925574, 16523049, 16133180, 11919560)
Baylor Genetics RCV003467571 SCV004204544 likely pathogenic Polycystic kidney disease 4 2024-02-21 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004800658 SCV005422316 uncertain significance not specified 2024-10-14 criteria provided, single submitter clinical testing Variant summary: PKHD1 c.5750A>G (p.Gln1917Arg) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5' splicing donor site. One predicts the variant weakens a 5' donor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 251178 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.5750A>G has been reported in the literature in individuals affected with kidney disorders (e.g.Adeva_2006, Bekheirnia_2021, Ward_2002). These data do not allow any conclusion about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 16523049, 35368817, 11919560). ClinVar contains an entry for this variant (Variation ID: 813380). Based on the evidence outlined above, the variant was classified as uncertain significance.
Fulgent Genetics, Fulgent Genetics RCV003467571 SCV005671857 uncertain significance Polycystic kidney disease 4 2024-02-12 criteria provided, single submitter clinical testing

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