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NM_014363.6(SACS):c.3074A>T (p.Asn1025Ile)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000193712.6
Variation ID:
193712
Description:
single nucleotide variant
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NM_014363.6(SACS):c.3074A>T (p.Asn1025Ile)

Allele ID
190875
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q12.12
Genomic location
13: 23340802 (GRCh38) GRCh38 UCSC
13: 23914941 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.23914941T>A
NC_000013.11:g.23340802T>A
NG_012342.1:g.97901A>T
... more HGVS
Protein change
N1025I, N878I
Other names
-
Canonical SPDI
NC_000013.11:23340801:T:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00086
The Genome Aggregation Database (gnomAD) 0.00102
The Genome Aggregation Database (gnomAD), exomes 0.00017
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00077
Exome Aggregation Consortium (ExAC) 0.00025
Links
ClinGen: CA239318
dbSNP: rs150981983
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Dec 4, 2020 RCV001080295.2
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Feb 14, 2019 RCV000173863.4
Likely benign 1 no assertion criteria provided May 2, 2020 RCV001277261.1
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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
Uncertain significance
(May 26, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000225027.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Feb 14, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001145330.1
Submitted: (Sep 25, 2019)
Evidence details
Likely benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia
Allele origin: germline
Invitae
Accession: SCV001006002.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(May 02, 2020)
no assertion criteria provided
Method: clinical testing
Charlevoix-Saguenay type spastic ataxia
Allele origin: germline
Natera, Inc.
Accession: SCV001464173.1
Submitted: (Dec 28, 2020)
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SACS - - - -

Text-mined citations for rs150981983...

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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