ClinVar Miner

Submissions for variant NM_015346.4(ZFYVE26):c.2338C>T (p.Arg780Ter)

dbSNP: rs941230062
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000671734 SCV000796745 likely pathogenic Hereditary spastic paraplegia 15 2017-12-22 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000671734 SCV002020940 pathogenic Hereditary spastic paraplegia 15 2021-01-22 criteria provided, single submitter clinical testing
DASA RCV000671734 SCV002107138 pathogenic Hereditary spastic paraplegia 15 2022-03-05 criteria provided, single submitter clinical testing The c.2338C>T;p.(Arg780*) variant creates a premature translational stop signal in the ZFYVE26 gene. It is expected to result in an absent or disrupted protein product - PVS1. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (PMID: 25497598) - PS4_supporting. This variant is not present in population databases (rs941230062- gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. The p.(Arg780*) was detected in trans with a pathogenic variant (PMID: 25497598) - PM3. In summary, the currently available evidence indicates that the variant is pathogenic.
Invitae RCV001855566 SCV002247333 pathogenic Spastic paraplegia 2023-12-01 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg780*) in the ZFYVE26 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ZFYVE26 are known to be pathogenic (PMID: 18394578, 19805727). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of hereditary spastic paraplegia (PMID: 25497598). ClinVar contains an entry for this variant (Variation ID: 555834). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

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