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NM_014363.6(SACS):c.5461T>C (p.Cys1821Arg)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 1, 2020
Accession:
VCV000696629.5
Variation ID:
696629
Description:
single nucleotide variant
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NM_014363.6(SACS):c.5461T>C (p.Cys1821Arg)

Allele ID
684405
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q12.12
Genomic location
13: 23338415 (GRCh38) GRCh38 UCSC
13: 23912554 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.11:g.23338415A>G
NC_000013.10:g.23912554A>G
NM_014363.6:c.5461T>C MANE Select NP_055178.3:p.Cys1821Arg missense
... more HGVS
Protein change
C1674R, C1821R
Other names
-
Canonical SPDI
NC_000013.11:23338414:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (G)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00078
Trans-Omics for Precision Medicine (TOPMed) 0.00006
Exome Aggregation Consortium (ExAC) 0.00088
The Genome Aggregation Database (gnomAD) 0.00003
1000 Genomes Project 0.00080
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Links
dbSNP: rs376680832
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Aug 16, 2019 RCV000863078.3
Benign 1 criteria provided, single submitter Dec 1, 2020 RCV001080973.2
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001115156.1
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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
Benign
(Aug 16, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001145337.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (3)
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Charlevoix-Saguenay spastic ataxia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001273109.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Dec 01, 2020)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia
Allele origin: germline
Invitae
Accession: SCV001003674.3
Submitted: (Jan 07, 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
Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan. Ilyas M BMC genomics 2015 PMID: 25887915
Exome sequencing identifies three novel candidate genes implicated in intellectual disability. Agha Z PloS one 2014 PMID: 25405613
Comparative analysis and functional mapping of SACS mutations reveal novel insights into sacsin repeated architecture. Romano A Human mutation 2013 PMID: 23280630

Text-mined citations for rs376680832...

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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 Jun 14, 2021