ClinVar Miner

Submissions for variant NM_025137.4(SPG11):c.1377C>T (p.Gly459=)

dbSNP: rs768183449
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000579056 SCV000681330 uncertain significance not provided 2018-01-08 criteria provided, single submitter clinical testing The c.1377C>T variant in the SPG11 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This change is predicted to create a new cryptic splice donor site in exon 6, and is expected to cause abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of c.1377C>T in this individual is unknown. The c.1377C>T variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.1377C>T as a variant of uncertain significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV000694835 SCV000823297 uncertain significance Hereditary spastic paraplegia 11 2021-09-01 criteria provided, single submitter clinical testing This sequence change affects codon 459 of the SPG11 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the SPG11 protein. This variant is present in population databases (rs768183449, ExAC 0.001%). This variant has not been reported in the literature in individuals affected with SPG11-related conditions. ClinVar contains an entry for this variant (Variation ID: 489333). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001848980 SCV002105660 uncertain significance Hereditary spastic paraplegia 2016-12-12 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002467903 SCV002764144 uncertain significance Amyotrophic lateral sclerosis type 5 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV002467904 SCV002764145 uncertain significance Charcot-Marie-Tooth disease axonal type 2X criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000694835 SCV002764146 uncertain significance Hereditary spastic paraplegia 11 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000579056 SCV005409927 uncertain significance not provided 2024-01-11 criteria provided, single submitter clinical testing PP3, PM2_moderate

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