ClinVar Miner

Submissions for variant NM_207346.3(TSEN54):c.1039A>T (p.Lys347Ter)

gnomAD frequency: 0.00003  dbSNP: rs143604970
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000760540 SCV000890431 likely pathogenic not provided 2018-03-13 criteria provided, single submitter clinical testing A variant that is likely pathogenic has been identified in the TSEN54 gene. The K347X variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The K347X nonsense variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The K347X variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.
Revvity Omics, Revvity RCV000760540 SCV002020312 likely pathogenic not provided 2021-04-03 criteria provided, single submitter clinical testing
Invitae RCV000760540 SCV002174870 pathogenic not provided 2023-12-17 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Lys347*) in the TSEN54 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TSEN54 are known to be pathogenic (PMID: 18711368, 20952379). This variant is present in population databases (rs143604970, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with TSEN54-related conditions. ClinVar contains an entry for this variant (Variation ID: 620188). For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV002493386 SCV002776249 likely pathogenic Pontocerebellar hypoplasia type 4; Pontocerebellar hypoplasia type 2A; Pontocerebellar hypoplasia type 5 2021-07-26 criteria provided, single submitter clinical testing

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