ClinVar Miner

Submissions for variant NM_003119.4(SPG7):c.1675A>T (p.Lys559Ter)

gnomAD frequency: 0.00001  dbSNP: rs372981030
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000198266 SCV000252329 likely pathogenic not provided 2021-01-28 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV000697812 SCV000826443 pathogenic Hereditary spastic paraplegia 7 2022-10-02 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Lys559*) in the SPG7 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SPG7 are known to be pathogenic (PMID: 21623769, 22964162). This variant is present in population databases (rs372981030, gnomAD 0.004%). This premature translational stop signal has been observed in individual(s) with clinical features of SPG7-related conditions (Invitae). ClinVar contains an entry for this variant (Variation ID: 215215). For these reasons, this variant has been classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen RCV000198266 SCV001246898 pathogenic not provided 2019-02-01 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001847888 SCV002105852 pathogenic Hereditary spastic paraplegia 2017-05-12 criteria provided, single submitter clinical testing
GenomeConnect - Invitae Patient Insights Network RCV000697812 SCV004037564 not provided Hereditary spastic paraplegia 7 no assertion provided phenotyping only Variant classified as Pathogenic and reported on 01-08-2018 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.

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