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NM_014363.6(SACS):c.9508C>T (p.Arg3170Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Sep 24, 2021)
Last evaluated:
Aug 23, 2020
Accession:
VCV000280094.7
Variation ID:
280094
Description:
single nucleotide variant
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NM_014363.6(SACS):c.9508C>T (p.Arg3170Ter)

Allele ID
264659
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q12.12
Genomic location
13: 23334368 (GRCh38) GRCh38 UCSC
13: 23908507 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.23908507G>A
NC_000013.11:g.23334368G>A
NG_012342.1:g.104335C>T
... more HGVS
Protein change
R3170*, R3023*
Other names
-
Canonical SPDI
NC_000013.11:23334367:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
Exome Aggregation Consortium (ExAC) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
ClinGen: CA6910613
dbSNP: rs202199411
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Jun 29, 2020 RCV000297710.5
Pathogenic 1 criteria provided, single submitter Aug 23, 2020 RCV001223182.2
Likely pathogenic 1 no assertion criteria provided Apr 5, 2016 RCV000411666.1
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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
1807 1899

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jun 29, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000329910.5
Submitted: (Sep 24, 2021)
Evidence details
Comment:
Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 1410 amino acids are lost, and other loss-of-function variants have been … (more)
Pathogenic
(Mar 11, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000843554.1
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (1)
Pathogenic
(Aug 23, 2020)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia
Allele origin: germline
Invitae
Accession: SCV001395319.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change results in a premature translational stop signal in the SACS gene (p.Arg3170*). While this is not anticipated to result in nonsense mediated … (more)
Likely pathogenic
(Apr 05, 2016)
no assertion criteria provided
Method: clinical testing
Charlevoix-Saguenay spastic ataxia
Allele origin: unknown
Counsyl
Accession: SCV000486037.2
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (1)

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
Diversity of ARSACS mutations in French-Canadians. Thiffault I The Canadian journal of neurological sciences. Le journal canadien des sciences neurologiques 2013 PMID: 23250129
Autosomal recessive spastic ataxia of Charlevoix-Saguenay: compound heterozygotes for nonsense mutations of the SACS gene. Narayanan V Journal of child neurology 2011 PMID: 21745802
Novel mutations in the sacsin gene in ataxia patients from Maritime Canada. Guernsey DL Journal of the neurological sciences 2010 PMID: 19892370

Text-mined citations for rs202199411...

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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 08, 2021