ClinVar Miner

Submissions for variant NM_025137.4(SPG11):c.5844del (p.Pro1949_Leu1950insTer)

dbSNP: rs1323156960
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000642563 SCV000764250 pathogenic Hereditary spastic paraplegia 11 2024-09-06 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu1950*) in the SPG11 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SPG11 are known to be pathogenic (PMID: 19105190, 20110243, 22154821, 26556829). This variant is present in population databases (no rsID available, gnomAD 0.004%). 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: 534866). For these reasons, this variant has been classified as Pathogenic.
Athena Diagnostics RCV001662692 SCV001880691 likely pathogenic not provided 2020-12-30 criteria provided, single submitter clinical testing This variant is expected to result in the loss of a functional protein. The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org).
Ambry Genetics RCV002358825 SCV002650862 pathogenic Inborn genetic diseases 2022-01-11 criteria provided, single submitter clinical testing The c.5844delT pathogenic mutation, located in coding exon 30 of the SPG11 gene, results from a deletion of one nucleotide at nucleotide position 5844, causing a translational frameshift with a predicted alternate stop codon (p.L1950*). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.
Genome-Nilou Lab RCV000642563 SCV002763787 likely pathogenic Hereditary spastic paraplegia 11 criteria provided, single submitter clinical testing

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