ClinVar Genomic variation as it relates to human health
NM_014946.4(SPAST):c.1495C>T (p.Arg499Cys)
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_014946.4(SPAST):c.1495C>T (p.Arg499Cys)
Variation ID: 5660 Accession: VCV000005660.45
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2p22.3 2: 32141905 (GRCh38) [ NCBI UCSC ] 2: 32366974 (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 Apr 4, 2013 Oct 20, 2024 Apr 4, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_014946.4:c.1495C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_055761.2:p.Arg499Cys missense NM_001363823.2:c.1492C>T NP_001350752.1:p.Arg498Cys missense NM_001363875.2:c.1396C>T NP_001350804.1:p.Arg466Cys missense NM_001377959.1:c.1399C>T NP_001364888.1:p.Arg467Cys missense NM_199436.2:c.1399C>T NP_955468.1:p.Arg467Cys missense NC_000002.12:g.32141905C>T NC_000002.11:g.32366974C>T NG_008730.1:g.83295C>T LRG_714:g.83295C>T LRG_714t1:c.1495C>T LRG_714p1:p.Arg499Cys Q9UBP0:p.Arg499Cys - Protein change
- R499C, R467C, R498C, R466C
- Other names
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- Canonical SPDI
- NC_000002.12:32141904:C:T
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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
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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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
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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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SPAST | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1330 | 1397 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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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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Apr 4, 2024 | RCV000006014.20 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 15, 2015 | RCV000415256.3 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jan 13, 2022 | RCV000523541.23 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Dec 12, 2016 | RCV001847585.4 |
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
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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
(Sep 15, 2015)
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criteria provided, single submitter
Method: clinical testing
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Spastic paraparesis
Affected status: yes
Allele origin:
unknown
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV000492797.1
First in ClinVar: Jan 13, 2017 Last updated: Jan 13, 2017 |
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Likely pathogenic
(Dec 12, 2016)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV002105612.1
First in ClinVar: Mar 19, 2022 Last updated: Mar 19, 2022 |
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Pathogenic
(Mar 21, 2022)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia 4
Affected status: yes
Allele origin:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002556973.2
First in ClinVar: Aug 08, 2022 Last updated: Dec 17, 2022 |
Comment:
The SPAST c.1495C>T variant is classified as Pathogenic (PS4_Moderate, PS3, PM2, PM5)
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Pathogenic
(Jan 13, 2022)
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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: SCV000617691.4
First in ClinVar: Dec 19, 2017 Last updated: Mar 04, 2023 |
Comment:
Published functional studies demonstrate a damaging effect on microtubule disassembly and ATPase activity (Errico et al., 2002; Evans et al., 2005); In silico analysis supports … (more)
Published functional studies demonstrate a damaging effect on microtubule disassembly and ATPase activity (Errico et al., 2002; Evans et al., 2005); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29980238, 31751864, 15716377, 29934652, 30780198, 30476002, 31285604, 28191889, 34950521, Varghaei2021[pdf], 21139634, 26094131, 17957230, 18701882, 11809724, 11309678, 10610178) (less)
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Pathogenic
(Apr 04, 2024)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia 4
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004809673.1
First in ClinVar: Apr 15, 2024 Last updated: Apr 15, 2024 |
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia 4
Affected status: yes
Allele origin:
unknown
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Paris Brain Institute, Inserm - ICM
Accession: SCV001450998.1
First in ClinVar: May 16, 2021 Last updated: May 16, 2021 |
Number of individuals with the variant: 1
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Pathogenic
(Apr 19, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia 4
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000645351.8
First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Arg499 amino acid residue in SPAST. Other variant(s) that disrupt this … (more)
For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Arg499 amino acid residue in SPAST. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 16009769, 16682546, 18701882, 20562464). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects SPAST function (PMID: 15716377). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 5660). This variant is also known as 1620C>T. This missense change has been observed in individuals with hereditary spastic paraplegia (HSP) (PMID: 10610178, 11309678, 12161613, 16055926, 17594340, 17957230, 19438933, 20718791, 25658484, 26208798, 27334366). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 499 of the SPAST protein (p.Arg499Cys). (less)
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Pathogenic
(Jul 17, 2023)
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criteria provided, single submitter
Method: clinical testing
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Hereditary spastic paraplegia 4
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV005086594.1
First in ClinVar: Jul 23, 2024 Last updated: Jul 23, 2024 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative and loss of function are … (more)
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative and loss of function are known mechanisms of disease for this gene and are associated with spastic paraplegia 4 (MIM#182601). Multiple loss of function variants have been reported, while a dominant negative mechanism has been stipulated for a small number of missense variants (ClinVar; PMID: 30006150). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance, but this is age-dependent and only a small proportion of individuals remain asymptomatic (PMID: 30476002). (I) 0115 - Variants in this gene are known to have variable expressivity, with variable age of onset and disease severity (PMID: 30476002). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to cysteine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0603 - Missense variant in a region that is highly intolerant to missense variation (high constraint region in DECIPHER). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported multiple times as pathogenic, and observed in individuals with hereditary spastic paraplegia, with an elevated risk of cognitive impairment (ClinVar, PMID: 29421991). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Pathogenic
(Sep 01, 2016)
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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: SCV001247360.26
First in ClinVar: May 09, 2020 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 1
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Pathogenic
(May 01, 2001)
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no assertion criteria provided
Method: literature only
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SPASTIC PARAPLEGIA 4
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000026196.2
First in ClinVar: Apr 04, 2013 Last updated: Oct 11, 2019 |
Comment on evidence:
In a member of a family with spastic paraplegia-4 (SPG4; 182601), Hazan et al. (1999) identified a heterozygous 1620C-T transition in exon 13 of the … (more)
In a member of a family with spastic paraplegia-4 (SPG4; 182601), Hazan et al. (1999) identified a heterozygous 1620C-T transition in exon 13 of the SPAST gene, resulting in an arg499-to-cys(R499C) substitution. This mutation was identified in family 618. Svenson et al. (2001) identified heterozygosity for the R499C mutation in another family segregating SPG4. (less)
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not provided
(-)
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no classification provided
Method: phenotyping only
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Hereditary spastic paraplegia 4
Affected status: unknown
Allele origin:
unknown
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GenomeConnect - Brain Gene Registry
Accession: SCV002760024.1
First in ClinVar: Dec 11, 2022 Last updated: Dec 11, 2022 |
Comment:
Variant interpreted as Pathogenic and reported on 07-18-2019 by Lab or GTR ID 26957. Assertions are reported exactly as they appear on the patient provided … (more)
Variant interpreted as Pathogenic and reported on 07-18-2019 by Lab or GTR ID 26957. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator John Constantino MD PhD from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. (less)
Clinical Features:
Phenotypic abnormality (present)
Age: 10-19 years
Sex: female
Method: Gene Panel Sequencing
Testing laboratory: GeneDx
Date variant was reported to submitter: 2019-07-18
Testing laboratory interpretation: Pathogenic
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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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Spastic paraplegia due to SPAST mutations is modified by the underlying mutation and sex. | Parodi L | Brain : a journal of neurology | 2018 | PMID: 30476002 |
Missense mutation of SPAST protein (I344K) results in loss of ATPase activity and prolonged the half-life, implicated in autosomal dominant hereditary spastic paraplegia. | Lim JH | Biochimica et biophysica acta. Molecular basis of disease | 2018 | PMID: 30006150 |
Association of Early-Onset Spasticity and Risk for Cognitive Impairment With Mutations at Amino Acid 499 in SPAST. | Gillespie MK | Journal of child neurology | 2018 | PMID: 29421991 |
SPAST mutation spectrum and familial occurrence among Czech patients with pure hereditary spastic paraplegia. | Mészárosová AU | Journal of human genetics | 2016 | PMID: 27334366 |
Mutational spectrum of the SPAST and ATL1 genes in Korean patients with hereditary spastic paraplegia. | Park H | Journal of the neurological sciences | 2015 | PMID: 26208798 |
Multimodal MRI-based study in patients with SPG4 mutations. | Rezende TJ | PloS one | 2015 | PMID: 25658484 |
Mutation screening of spastin, atlastin, and REEP1 in hereditary spastic paraplegia. | McCorquodale DS 3rd | Clinical genetics | 2011 | PMID: 20718791 |
Hereditary spastic paraplegia due to SPAST mutations in 151 Dutch patients: new clinical aspects and 27 novel mutations. | de Bot ST | Journal of neurology, neurosurgery, and psychiatry | 2010 | PMID: 20562464 |
Tunisian hereditary spastic paraplegias: clinical variability supported by genetic heterogeneity. | Boukhris A | Clinical genetics | 2009 | PMID: 19438933 |
Expansion of mutation spectrum, determination of mutation cluster regions and predictive structural classification of SPAST mutations in hereditary spastic paraplegia. | Shoukier M | European journal of human genetics : EJHG | 2009 | PMID: 18701882 |
Mental deficiency in three families with SPG4 spastic paraplegia. | Ribaï P | European journal of human genetics : EJHG | 2008 | PMID: 17957230 |
Seven novel mutations and four exon deletions in a collection of Norwegian patients with SPG4 hereditary spastic paraplegia. | Erichsen AK | European journal of neurology | 2007 | PMID: 17594340 |
Eight novel mutations in SPG4 in a large sample of patients with hereditary spastic paraplegia. | Crippa F | Archives of neurology | 2006 | PMID: 16682546 |
Spastin mutations are frequent in sporadic spastic paraparesis and their spectrum is different from that observed in familial cases. | Depienne C | Journal of medical genetics | 2006 | PMID: 16055926 |
Mutation analysis of SPG4 and SPG3A genes and its implication in molecular diagnosis of Korean patients with hereditary spastic paraplegia. | Park SY | Archives of neurology | 2005 | PMID: 16009769 |
Linking axonal degeneration to microtubule remodeling by Spastin-mediated microtubule severing. | Evans KJ | The Journal of cell biology | 2005 | PMID: 15716377 |
Spastin gene mutation in Japanese with hereditary spastic paraplegia. | Yabe I | Journal of medical genetics | 2002 | PMID: 12161613 |
Identification and expression analysis of spastin gene mutations in hereditary spastic paraplegia. | Svenson IK | American journal of human genetics | 2001 | PMID: 11309678 |
Spastin, a new AAA protein, is altered in the most frequent form of autosomal dominant spastic paraplegia. | Hazan J | Nature genetics | 1999 | PMID: 10610178 |
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Text-mined citations for rs121908511 ...
HelpRecord last updated Oct 20, 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.