ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.8863C>T (p.Arg2955Ter)

dbSNP: rs1229564017
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001386809 SCV001587157 pathogenic Autosomal recessive polycystic kidney disease 2023-12-13 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg2955*) in the PKHD1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PKHD1 are known to be pathogenic (PMID: 19940839). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of polycystic kidney disease (PMID: 31730820). ClinVar contains an entry for this variant (Variation ID: 1073734). For these reasons, this variant has been classified as Pathogenic.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV002471106 SCV002769175 pathogenic Polycystic kidney disease 4 2020-05-26 criteria provided, single submitter clinical testing Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0106 - This gene is known to be associated with autosomal recessive disease. (N) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (located in exon 57 of 67). (P) 0251 - Variant is heterozygous. (N) 0301 - Variant is absent from gnomAD. (P) 0701 - Comparable variants have very strong previous evidence for pathogenicity. Multiple NMD-predicted variants have been reported as pathogenic (ClinVar) (P) 0807 - Variant has not previously been reported in a clinical context. (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1201 - Heterozygous variant detected in trans with a second (at least likely) pathogenic heterozygous variant in a recessive disease. (P) 1206 - Variant is paternally inherited. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign
Baylor Genetics RCV002471106 SCV004204578 pathogenic Polycystic kidney disease 4 2023-12-04 criteria provided, single submitter clinical testing
Natera, Inc. RCV001386809 SCV002077965 pathogenic Autosomal recessive polycystic kidney disease 2020-10-08 no assertion criteria provided clinical testing

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