ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.2180dup (p.Asn727fs)

dbSNP: rs1554212326
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000588451 SCV000699855 likely pathogenic Autosomal recessive polycystic kidney disease 2017-02-03 criteria provided, single submitter clinical testing Variant summary: The PKHD1 c.2180dupA (p.Asn727Lysfs) variant results in a premature termination codon, predicted to cause a truncated or absent PKHD1 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (e.g. c.3761_3762delinsG, p.Ala1254fs). One in silico tool predicts a damaging outcome for this variant. This variant is absent in 121276 control chromosomes and has been reported in at least one affected individual in the literature. Taken together, this variant is classified as likely pathogenic.
Invitae RCV000588451 SCV002234424 pathogenic Autosomal recessive polycystic kidney disease 2023-08-29 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Asn727Lysfs*39) 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 polycystic kidney disease (PMID: 15805161). ClinVar contains an entry for this variant (Variation ID: 496517). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic.
Counsyl RCV000588451 SCV001132269 likely pathogenic Autosomal recessive polycystic kidney disease 2015-10-22 no assertion criteria provided clinical testing
Natera, Inc. RCV000588451 SCV002081042 likely pathogenic Autosomal recessive polycystic kidney disease 2021-03-22 no assertion criteria provided clinical testing

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