ClinVar Miner

Submissions for variant NM_017882.3(CLN6):c.150C>G (p.Tyr50Ter) (rs154774640)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000058908 SCV000568366 likely pathogenic not provided 2017-03-08 criteria provided, single submitter clinical testing The Y50X variant was identified in a patient with a clinical diagnosis of Kufs disease who was also heterozygous for two missense substitutions in the CLN6 gene, although no further clinical details were provided and parental testing was not performed to determine the phase of the three variants (Arsov et al., 2011). The Y50X variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. It is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret Y50X as a likely pathogenic variant.
Invitae RCV000702360 SCV000831212 pathogenic Neuronal ceroid lipofuscinosis 2020-10-31 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr50*) in the CLN6 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individuals affected with neuronal ceroid lipofuscinosis (PMID: 26075876, 21549341). ClinVar contains an entry for this variant (Variation ID: 68094). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Loss-of-function variants in CLN6 are known to be pathogenic (PMID: 19135028). For these reasons, this variant has been classified as Pathogenic.
SNPedia RCV000058908 SCV000090429 not provided not provided no assertion provided not provided
Counsyl RCV000668229 SCV000792797 likely pathogenic Neuronal ceroid lipofuscinosis 6 2017-07-14 no assertion criteria provided clinical testing

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