ClinVar Miner

Submissions for variant NM_000310.4(PPT1):c.455del (p.Cys152fs)

dbSNP: rs886041568
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000356077 SCV000330249 pathogenic not provided 2016-03-04 criteria provided, single submitter clinical testing The c.455delG pathogenic variant in the PPT1 gene has not been reported previously as a pathogenicvariant nor as a benign variant, to our knowledge. This variant causes a frameshift starting with codonCysteine 152, changes this amino acid to a Serine residue, and creates a premature Stop codon atposition 16 of the new reading frame, denoted p.Cys152SerfsX16. This variant is predicted to causeloss of normal protein function either through protein truncation or nonsense-mediated mRNA decay.The c.455delG variant was not observed in approximately 6500 individuals of European and AfricanAmerican ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benignvariant in these populations. We interpret c.455delG as a pathogenic variant.
Baylor Genetics RCV000984304 SCV004204131 pathogenic Neuronal ceroid lipofuscinosis 1 2023-10-14 criteria provided, single submitter clinical testing
Invitae RCV000984304 SCV004614016 pathogenic Neuronal ceroid lipofuscinosis 1 2023-06-12 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 280344). This variant has not been reported in the literature in individuals affected with PPT1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Cys152Serfs*16) in the PPT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PPT1 are known to be pathogenic (PMID: 10679943, 21990111).
Counsyl RCV000984304 SCV001132476 likely pathogenic Neuronal ceroid lipofuscinosis 1 2015-02-11 no assertion criteria provided clinical testing

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