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NM_014363.6(SACS):c.9562T>C (p.Phe3188Leu)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: May 26, 2021)
Last evaluated:
Dec 3, 2020
Accession:
VCV000586446.6
Variation ID:
586446
Description:
single nucleotide variant
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NM_014363.6(SACS):c.9562T>C (p.Phe3188Leu)

Allele ID
577309
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
13q12.12
Genomic location
13: 23334314 (GRCh38) GRCh38 UCSC
13: 23908453 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000013.10:g.23908453A>G
NC_000013.11:g.23334314A>G
NG_012342.1:g.104389T>C
... more HGVS
Protein change
F3188L, F3041L
Other names
-
Canonical SPDI
NC_000013.11:23334313:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (G)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00028
The Genome Aggregation Database (gnomAD) 0.00010
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Trans-Omics for Precision Medicine (TOPMed) 0.00018
1000 Genomes Project 0.00100
Exome Aggregation Consortium (ExAC) 0.00026
Links
dbSNP: rs137905181
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Sep 2, 2019 RCV000712994.3
Uncertain significance 2 criteria provided, single submitter Oct 31, 2018 RCV000765118.2
Likely benign 1 criteria provided, single submitter Dec 3, 2020 RCV001034278.2
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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
Uncertain significance
(Mar 15, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000843555.1
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Charlevoix-Saguenay spastic ataxia
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000896340.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Likely benign
(Dec 03, 2020)
criteria provided, single submitter
Method: clinical testing
Spastic paraplegia
Allele origin: germline
Invitae
Accession: SCV001197616.2
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Sep 02, 2019)
criteria provided, single submitter
Method: clinical testing
Not provided
Allele origin: germline
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV001713615.1
Submitted: (May 26, 2021)
Evidence details
Likely benign
(Jun 16, 2020)
no assertion criteria provided
Method: clinical testing
Charlevoix-Saguenay type spastic ataxia
Allele origin: germline
Natera, Inc.
Accession: SCV001455920.1
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
Probable Diagnosis of a Patient with Niemann-Pick Disease Type C: Managing Pitfalls of Exome Sequencing. Zeiger WA JIMD reports 2018 PMID: 29453517
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868

Text-mined citations for rs137905181...

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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 Sep 29, 2021