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NM_014363.6(SACS):c.2439_2440del (p.Val815fs)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: May 20, 2021)
Last evaluated:
Oct 23, 2020
Accession:
VCV000188856.12
Variation ID:
188856
Description:
2bp deletion
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NM_014363.6(SACS):c.2439_2440del (p.Val815fs)

Allele ID
186871
Variant type
Deletion
Variant length
2 bp
Cytogenetic location
13q12.12
Genomic location
13: 23341436-23341437 (GRCh38) GRCh38 UCSC
13: 23915575-23915576 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.23915575_23915576del
NC_000013.11:g.23341436_23341437del
NG_012342.1:g.97266_97267del
... more HGVS
Protein change
V815fs, V668fs
Other names
-
Canonical SPDI
NC_000013.11:23341435:AT:
Functional consequence
No function
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD) 0.00003
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD), exomes 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00008
Links
ClinGen: CA274046
dbSNP: rs775059063
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 Mar 1, 2020 RCV000169208.2
Pathogenic 2 criteria provided, multiple submitters, no conflicts Oct 23, 2020 RCV000992783.2
Pathogenic 1 criteria provided, single submitter May 3, 2020 RCV001382654.1
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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 27, 2014)
criteria provided, single submitter
Method: literature only
Spastic ataxia Charlevoix-Saguenay type
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220462.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (1)
Pathogenic
(Jul 08, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001145324.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (1)
Comment:
The variant results in a shift of the reading frame, and is therefore predicted to result in the loss of a functional protein. Found in … (more)
Pathogenic
(Oct 23, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
(Unknown mechanism)
Allele origin: germline
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV001448098.1
Submitted: (Oct 23, 2020)
Evidence details
Pathogenic
(May 03, 2020)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia
Allele origin: germline
Invitae
Accession: SCV001581541.1
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.Val815Glyfs*4). While this is not anticipated to result in nonsense mediated … (more)
Pathogenic
(Mar 01, 2020)
criteria provided, single submitter
Method: clinical testing
Charlevoix-Saguenay spastic ataxia
(Autosomal recessive inheritance)
Allele origin: inherited
Medical Genetics Laboratory,Tarbiat Modares University
Accession: SCV001622768.1
Submitted: (May 20, 2021)
Evidence details

Functional evidence

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Functional consequence Method Result Submitter Supporting information
No function
Medical Genetics Laboratory,Tarbiat Modares University
Accession: SCV001622768.1
Submitted: (May 20, 2021)
Evidence details

Citations for this variant

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Title Author Journal Year Link
Exome sequencing: an efficient diagnostic tool for complex neurodegenerative disorders. Hammer MB European journal of neurology 2013 PMID: 23043354
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 rs775059063...

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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 16, 2021