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NM_000368.5(TSC1):c.3387C>T (p.Ala1129=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(3);Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 4, 2020
Accession:
VCV000064816.9
Variation ID:
64816
Description:
single nucleotide variant
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NM_000368.5(TSC1):c.3387C>T (p.Ala1129=)

Allele ID
75745
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.13
Genomic location
9: 132896343 (GRCh38) GRCh38 UCSC
9: 135771730 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_001162427.2:c.3234C>T NP_001155899.1:p.Ala1078= synonymous
NM_001362177.2:c.3024C>T NP_001349106.1:p.Ala1008= synonymous
NC_000009.11:g.135771730G>A
... more HGVS
Protein change
-
Other names
p.A1129A:GCC>GCT
Canonical SPDI
NC_000009.12:132896342:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00220 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00100
Trans-Omics for Precision Medicine (TOPMed) 0.00009
1000 Genomes Project 0.00220
The Genome Aggregation Database (gnomAD) 0.00007
Trans-Omics for Precision Medicine (TOPMed) 0.00007
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD), exomes 0.00093
Links
ClinGen: CA007340
Tuberous sclerosis database (TSC1): TSC1_00421
dbSNP: rs200200869
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 4, 2020 RCV000234681.8
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000296323.2
Benign 1 criteria provided, single submitter Jun 6, 2016 RCV000563418.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Jan 28, 2016 RCV000193910.4
not provided 1 no assertion provided - RCV000055007.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TSC1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2813 2857

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(May 15, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000249204.1
Submitted: (Sep 15, 2015)
Evidence details
Benign
(Sep 10, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000169098.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Tuberous sclerosis 1
Allele origin: germline
Invitae
Accession: SCV000284723.7
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 28, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000339180.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Tuberous sclerosis 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000478173.3
Submitted: (Feb 20, 2020)
Evidence details
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)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Focal cortical dysplasia type II
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000478174.3
Submitted: (Feb 20, 2020)
Evidence details
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
(Jun 06, 2016)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000675376.3
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Co-occurence with mutation in same gene (phase unknown);Internal frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance;Other data supporting … (more)
not provided
(-)
no assertion provided
Method: curation
TSC
Allele origin: germline
Tuberous sclerosis database (TSC1)
Accession: SCV000083225.2
Submitted: (Aug 09, 2013)
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=TSC1 - - - -

Text-mined citations for rs200200869...

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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 Dec 04, 2021