ClinVar Genomic variation as it relates to human health
NM_025137.4(SPG11):c.4307_4308del (p.Gln1436fs)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_025137.4(SPG11):c.4307_4308del (p.Gln1436fs)
Variation ID: 41315 Accession: VCV000041315.47
- Type and length
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Deletion, 2 bp
- Location
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Cytogenetic: 15q21.1 15: 44596209-44596210 (GRCh38) [ NCBI UCSC ] 15: 44888407-44888408 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline May 3, 2013 Oct 26, 2024 Jan 9, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_025137.4:c.4307_4308del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_079413.3:p.Gln1436fs frameshift NM_025137.4:c.4307_4308delAA MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NM_001160227.2:c.4307_4308del NP_001153699.1:p.Gln1436fs frameshift NC_000015.10:g.44596209_44596210del NC_000015.9:g.44888407_44888408del NG_008885.1:g.72469_72470del - Protein change
- Q1436fs
- Other names
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- Canonical SPDI
- NC_000015.10:44596208:TT:
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Exome Aggregation Consortium (ExAC) 0.00005
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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LOC130056973 | - | - | - | GRCh38 | - | 55 |
SPG11 | - | - |
GRCh38 GRCh37 |
3255 | 3356 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (7) |
criteria provided, multiple submitters, no conflicts
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Jan 9, 2024 | RCV000034216.22 | |
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Jun 30, 2023 | RCV000517443.27 | |
Pathogenic (1) |
criteria provided, single submitter
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Dec 14, 2022 | RCV002326720.3 | |
Likely pathogenic (1) |
no assertion criteria provided
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Jun 1, 2022 | RCV004767029.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Mar 28, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Athena Diagnostics
Accession: SCV000615417.1
First in ClinVar: Dec 19, 2017 Last updated: Dec 19, 2017 |
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Pathogenic
(Jan 10, 2019)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia 11
Affected status: yes
Allele origin:
unknown
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV001370048.2
First in ClinVar: Jul 06, 2020 Last updated: Dec 12, 2020 |
Comment:
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2,PP5.
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia 11
Affected status: unknown
Allele origin:
germline
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Genome-Nilou Lab
Accession: SCV002763914.1
First in ClinVar: Dec 17, 2022 Last updated: Dec 17, 2022 |
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Pathogenic
(Jun 30, 2023)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV003936463.1
First in ClinVar: Jul 08, 2023 Last updated: Jul 08, 2023 |
Comment:
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of … (more)
Frameshift 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 significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 18586399, 30081747, 19105190, 24482476, 29980238, 26374131, 24833714, 18079167, 31589614, 32214227, 33098801, 33619735, 35872528) (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia 11
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV004100340.1
First in ClinVar: Nov 04, 2023 Last updated: Nov 04, 2023 |
Comment:
The frameshift deletion p.Q1436Rfs*7 in SPG11 (NM_025137.4) has been reported to ClinVar as Pathogenic. This variant has been observed in individuals affected with autosomal recessive … (more)
The frameshift deletion p.Q1436Rfs*7 in SPG11 (NM_025137.4) has been reported to ClinVar as Pathogenic. This variant has been observed in individuals affected with autosomal recessive hereditary spastic paraplegia and to segregate with disease in a family (Stevanin G et al, 2008; Novarino G et al, 2014). The p.Q1436Rfs*7 variant is observed in 1/16,256 (0.0062%) alleles from individuals of African background in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant is predicted to cause loss of normal protein function through protein truncation caused a frameshift mutation. The frame shifted sequence continues 7 residues until a stop codon is reached. The gene SPG11 has a low rate of benign loss of function variants as indicated by a high LoF variants Z-Score of 3.29. The p.Q1436Rfs*7 variant is a loss of function variant in the gene SPG11, which is intolerant of Loss of Function variants, as indicated by the presence of existing pathogenic loss of function variant NP_079413.3:p.L68Ffs*2 and 156 others. There are 83 downstream pathogenic loss of function variants, with the furthest variant being 952 residues downstream of the variant p.Q1436Rfs*7. For these reasons, this variant has been classified as Pathogenic. (less)
Clinical Features:
Difficulty walking (present) , Weak grip (present) , Difficulty standing (present)
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Pathogenic
(Oct 23, 2020)
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criteria provided, single submitter
Method: clinical testing
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not provided
(Unknown mechanism)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001448124.1
First in ClinVar: Nov 28, 2020 Last updated: Nov 28, 2020 |
Clinical Features:
Spastic paraplegia (present) , Urinary urgency (present) , Spasticity (present) , Lower limb spasticity (present) , Gait ataxia (present) , Hyperactive deep tendon reflexes (present)
Sex: female
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Pathogenic
(Jun 25, 2021)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia 11
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
paternal,
inherited
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Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
Accession: SCV001149939.2
First in ClinVar: Feb 03, 2020 Last updated: Dec 24, 2022 |
Observation 1:
Number of individuals with the variant: 1
Clinical Features:
Dysarthria (present) , Arthralgia of the hip (present) , Nystagmus (present) , Tip-toe gait (present) , Cerebellar ataxia (present)
Observation 2:
Number of individuals with the variant: 1
Clinical Features:
Dysarthria (present) , Spastic paraparesis (present) , Tremor (present) , Dystonic disorder (present)
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Pathogenic
(Jan 09, 2024)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia 11
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001388063.5
First in ClinVar: Jul 16, 2020 Last updated: Feb 28, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Gln1436Argfs*7) in the SPG11 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Gln1436Argfs*7) 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 (rs312262759, gnomAD 0.02%). This premature translational stop signal has been observed in individual(s) with autosomal recessive hereditary spastic paraplegia (PMID: 18079167, 24482476). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 41315). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Dec 14, 2022)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002627557.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The c.4307_4308delAA (p.Q1436Rfs*7) alteration, located in exon 25 (coding exon 25) of the SPG11 gene, consists of a deletion of 2 nucleotides from position 4307 … (more)
The c.4307_4308delAA (p.Q1436Rfs*7) alteration, located in exon 25 (coding exon 25) of the SPG11 gene, consists of a deletion of 2 nucleotides from position 4307 to 4308, causing a translational frameshift with a predicted alternate stop codon after 7 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on data from gnomAD, the c.4307_4308delAA (p.Q1436Rfs*7) alteration has an overall frequency of 0.004% (10/282800) total alleles studied. The highest observed frequency was 0.012% (3/24962) of African alleles. This alteration has been detected in the homozygous state or in conjunction with a second disease-causing allele in multiple individuals with SPG11-related neurologic disorders (Stevanin, 2008; Lynch, 2016; Pensato, 2014; Denora, 2009; Chen, 2008; Hengel 2020; Zech 2020; Shi 2022; Utz 2022; Dosi, 2021). Based on the available evidence, this alteration is classified as pathogenic. (less)
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Pathogenic
(Sep 01, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001249035.26
First in ClinVar: May 12, 2020 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 1
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Likely pathogenic
(Jun 01, 2022)
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no assertion criteria provided
Method: provider interpretation
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Charcot-Marie-Tooth disease axonal type 2X
Affected status: yes
Allele origin:
inherited
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Solve-RD Consortium
Accession: SCV005200072.1
First in ClinVar: Oct 26, 2024 Last updated: Oct 26, 2024
Comment:
Variant identified during reanalysis of unsolved cases by the Solve-RD project. The Solve-RD project has received funding from the European Union’s Horizon 2020 research and … (more)
Variant identified during reanalysis of unsolved cases by the Solve-RD project. The Solve-RD project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 779257. (less)
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Comment:
Variant confirmed as disease-causing by referring clinical team
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Pathogenic
(Aug 01, 2019)
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no assertion criteria provided
Method: research
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Hereditary spastic paraplegia 11
Affected status: yes
Allele origin:
germline
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Section for Clinical Neurogenetics, University of Tübingen
Accession: SCV001156107.1
First in ClinVar: Apr 06, 2020 Last updated: Apr 06, 2020 |
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not provided
(-)
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no classification provided
Method: literature only
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Hereditary spastic paraplegia 11
Affected status: not provided
Allele origin:
unknown
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GeneReviews
Accession: SCV000058154.3
First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Neuropsychology and MRI correlates of neurodegeneration in SPG11 hereditary spastic paraplegia. | Utz KS | Orphanet journal of rare diseases | 2022 | PMID: 35906604 |
Clinical Features and Genetic Spectrum of Patients With Clinically Suspected Hereditary Progressive Spastic Paraplegia. | Shi Y | Frontiers in neurology | 2022 | PMID: 35572931 |
Neuroimaging patterns in paediatric onset hereditary spastic paraplegias. | Dosi C | Journal of the neurological sciences | 2021 | PMID: 33866115 |
Monogenic variants in dystonia: an exome-wide sequencing study. | Zech M | The Lancet. Neurology | 2020 | PMID: 33098801 |
First-line exome sequencing in Palestinian and Israeli Arabs with neurological disorders is efficient and facilitates disease gene discovery. | Hengel H | European journal of human genetics : EJHG | 2020 | PMID: 32214227 |
Spastic Paraplegia 11. | Adam MP | - | 2019 | PMID: 20301389 |
ALS5/SPG11/KIAA1840 mutations cause autosomal recessive axonal Charcot-Marie-Tooth disease. | Montecchiani C | Brain : a journal of neurology | 2016 | PMID: 26556829 |
Hereditary spastic paraplegia in Greece: characterisation of a previously unexplored population using next-generation sequencing. | Lynch DS | European journal of human genetics : EJHG | 2016 | PMID: 26374131 |
Overlapping phenotypes in complex spastic paraplegias SPG11, SPG15, SPG35 and SPG48. | Pensato V | Brain : a journal of neurology | 2014 | PMID: 24833714 |
Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. | Novarino G | Science (New York, N.Y.) | 2014 | PMID: 24482476 |
Exome sequencing reveals SPG11 mutations causing juvenile ALS. | Daoud H | Neurobiology of aging | 2012 | PMID: 22154821 |
SPATACSIN mutations cause autosomal recessive juvenile amyotrophic lateral sclerosis. | Orlacchio A | Brain : a journal of neurology | 2010 | PMID: 20110243 |
Screening of ARHSP-TCC patients expands the spectrum of SPG11 mutations and includes a large scale gene deletion. | Denora PS | Human mutation | 2009 | PMID: 19105190 |
Diffusion tensor imaging of two unrelated Chinese men with hereditary spastic paraplegia associated with thin corpus callosum. | Chen Q | Neuroscience letters | 2008 | PMID: 18586399 |
Two novel mutations in the SPG11 gene causing hereditary spastic paraplegia associated with thin corpus callosum. | Zhang SS | Movement disorders : official journal of the Movement Disorder Society | 2008 | PMID: 18361476 |
Mutations in SPG11 are frequent in autosomal recessive spastic paraplegia with thin corpus callosum, cognitive decline and lower motor neuron degeneration. | Stevanin G | Brain : a journal of neurology | 2008 | PMID: 18079167 |
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Text-mined citations for rs312262759 ...
HelpRecord last updated Oct 27, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.