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NM_014363.6(SACS):c.12160C>T (p.Gln4054Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 30, 2021)
Last evaluated:
Dec 13, 2019
Accession:
VCV000038458.16
Variation ID:
38458
Description:
single nucleotide variant
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NM_014363.6(SACS):c.12160C>T (p.Gln4054Ter)

Allele ID
47016
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q12.12
Genomic location
13: 23331716 (GRCh38) GRCh38 UCSC
13: 23905855 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.23905855G>A
NC_000013.11:g.23331716G>A
NG_012342.1:g.106987C>T
... more HGVS
Protein change
Q4054*, Q3907*
Other names
-
Canonical SPDI
NC_000013.11:23331715:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00002
Links
ClinGen: CA343113
dbSNP: rs281865120
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, single submitter Apr 5, 2016 RCV000032008.2
Likely pathogenic 4 criteria provided, single submitter Sep 1, 2016 RCV000487627.7
Pathogenic 1 criteria provided, single submitter Dec 13, 2019 RCV001044731.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SACS - - GRCh38
GRCh37
1808 1900

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Dec 13, 2019)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia
Allele origin: germline
Invitae
Accession: SCV001208544.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change results in a premature translational stop signal in the SACS gene (p.Gln4054*). While this is not anticipated to result in nonsense mediated … (more)
Pathogenic
(Apr 05, 2016)
criteria provided, single submitter
Method: clinical testing
Charlevoix-Saguenay spastic ataxia
Allele origin: unknown
Counsyl
Accession: SCV000486129.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (1)
Likely pathogenic
(Sep 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000574948.12
Submitted: (Jul 04, 2021)
Evidence details
Pathogenic
(Dec 19, 2019)
no assertion criteria provided
Method: literature only
Charlevoix-Saguenay spastic ataxia
Allele origin: germline
GeneReviews
Accession: SCV000054717.2
Submitted: (Feb 08, 2021)
Evidence details
Publications
PubMed (2)
BookShelf: NBK1255
Pathogenic
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Human Genetics - Radboudumc,Radboudumc
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001956156.1
Submitted: (Sep 30, 2021)
Evidence details
Pathogenic
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001809522.1
Submitted: (Aug 24, 2021)
Evidence details
Pathogenic
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001741296.3
Submitted: (Sep 02, 2021)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
ARSACS Vermeer S - 2020 PMID: 20301432
A reduction in Drp1-mediated fission compromises mitochondrial health in autosomal recessive spastic ataxia of Charlevoix Saguenay. Bradshaw TY Human molecular genetics 2016 PMID: 27288452
New practical definitions for the diagnosis of autosomal recessive spastic ataxia of Charlevoix-Saguenay. Pilliod J Annals of neurology 2015 PMID: 26288984
Autosomal recessive spastic ataxia of Charlevoix Saguenay (ARSACS): expanding the genetic, clinical and imaging spectrum. Synofzik M Orphanet journal of rare diseases 2013 PMID: 23497566
ARSACS in the Dutch population: a frequent cause of early-onset cerebellar ataxia. Vermeer S Neurogenetics 2008 PMID: 18465152
Sacsin-related ataxia caused by the novel nonsense mutation Arg4325X. Yamamoto Y Journal of neurology 2006 PMID: 16944349

Text-mined citations for rs281865120...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 07, 2021