ClinVar Miner

Submissions for variant NM_025137.4(SPG11):c.6598A>T (p.Lys2200Ter)

gnomAD frequency: 0.00006  dbSNP: rs141263564
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000694024 SCV000822449 pathogenic Hereditary spastic paraplegia 11 2023-04-22 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 572602). This premature translational stop signal has been observed in individual(s) with hereditary spastic paraplegia (PMID: 23733235). This variant is present in population databases (rs141263564, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Lys2200*) 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).
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001849059 SCV002105759 pathogenic Hereditary spastic paraplegia 2016-12-12 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000694024 SCV002763692 pathogenic Hereditary spastic paraplegia 11 criteria provided, single submitter clinical testing
Genetics and Molecular Pathology, SA Pathology RCV003447554 SCV004175441 pathogenic Early-onset Parkinson disease 20 2023-02-15 criteria provided, single submitter clinical testing
Molecular Genetics Lab, CHRU Brest RCV003883160 SCV004697603 pathogenic Amyotrophic lateral sclerosis type 5; Hereditary spastic paraplegia 11; Charcot-Marie-Tooth disease axonal type 2X criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV004792389 SCV005414258 pathogenic not provided 2024-07-30 criteria provided, single submitter clinical testing PM2, PM3, PVS1
PreventionGenetics, part of Exact Sciences RCV003411614 SCV004113359 pathogenic SPG11-related disorder 2024-09-05 no assertion criteria provided clinical testing The SPG11 c.6598A>T variant is predicted to result in premature protein termination (p.Lys2200*). This variant was reported in the compound heterozygous state with another loss-of-function variant in two patients with autosomal recessive spastic paraplegia (Yoon et al. 2013. PubMed ID: 23733235; Carrasco Salas et al. 2022. PubMed ID: 33059505). This variant is reported in 0.0039% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Nonsense variants in SPG11 are expected to be pathogenic. This variant is interpreted as pathogenic.
Solve-RD Consortium RCV004768574 SCV005091440 likely pathogenic Charcot-Marie-Tooth disease axonal type 2X 2022-06-01 no assertion criteria provided provider interpretation Variant confirmed as disease-causing by referring clinical team

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