ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.4415delinsTATTCCCC (p.Cys1472fs)

dbSNP: rs398124486
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000177670 SCV000229574 pathogenic not provided 2014-08-29 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001244749 SCV001417992 pathogenic Autosomal recessive polycystic kidney disease 2022-03-19 criteria provided, single submitter clinical testing This variant is also known as c.4415-4418del4ins11, c.4415_4418del4insTATTCCCCTCT. This premature translational stop signal has been observed in individual(s) with autosomal recessive polycystic kidney disease (PMID: 15805161). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change creates a premature translational stop signal (p.Cys1472Leufs*36) 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). For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV001781409 SCV002018815 pathogenic Polycystic kidney disease 4 2021-09-03 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001781409 SCV002813813 pathogenic Polycystic kidney disease 4 2021-11-08 criteria provided, single submitter clinical testing
Baylor Genetics RCV001781409 SCV004204788 pathogenic Polycystic kidney disease 4 2022-06-22 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000177670 SCV003839874 pathogenic not provided 2022-06-02 no assertion criteria provided clinical testing DNA sequence analysis of the PKHD1 gene demonstrated a deletion of one base pair and the insertion of eight base pairs in exon 32, c.4415delinsTATTCCCC. This sequence change results in an amino acid frameshift and creates a premature stop codon 36 amino acids downstream of the change, p.Cys1472Leufs*36. This sequence change is predicted to result in an abnormal transcript, which may be degraded, or may lead to the production of a truncated PKHD1 protein with potentially abnormal function. This sequence change has not been described in population databases such as ExAC and gnomAD. A similar sequence change, c.4415_4418del4ins11TATTCCCCTCT, predicted to lead to the same amino acid frameshift, has previously been described in an individual with autosomal recessive polycystic kidney disease (PMID: 15805161). Collectively, these evidences indicate this sequence change is pathogenic.

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