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NM_000368.5(TSC1):c.1231C>A (p.Leu411Ile)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000064790.5
Variation ID:
64790
Description:
single nucleotide variant
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NM_000368.5(TSC1):c.1231C>A (p.Leu411Ile)

Allele ID
75719
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.13
Genomic location
9: 132910603 (GRCh38) GRCh38 UCSC
9: 135785990 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
Q92574:p.Leu411Ile
NC_000009.11:g.135785990G>T
LRG_486:g.39031C>A
... more HGVS
Protein change
L411I, L290I, L360I, L410I
Other names
-
Canonical SPDI
NC_000009.12:132910602:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00000
Exome Aggregation Consortium (ExAC) 0.00001
The Genome Aggregation Database (gnomAD) 0.00003
Links
ClinGen: CA004502
UniProtKB: Q92574#VAR_070650
Tuberous sclerosis database (TSC1): TSC1_00469
dbSNP: rs397514840
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 Dec 7, 2020 RCV000474632.4
Uncertain significance 1 criteria provided, single submitter Nov 15, 2016 RCV000761088.1
not provided 1 no assertion provided - RCV000054977.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
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
(Nov 15, 2016)
criteria provided, single submitter
Method: clinical testing
Craniopharyngioma
Allele origin: germline
St. Jude Clinical Genomics Lab, St. Jude Children's Research Hospital
Accession: SCV000891003.1
Submitted: (Dec 04, 2018)
Evidence details
Benign
(Dec 07, 2020)
criteria provided, single submitter
Method: clinical testing
Tuberous sclerosis 1
Allele origin: germline
Invitae
Accession: SCV000552325.5
Submitted: (Jan 07, 2021)
Evidence details
not provided
(-)
no assertion provided
Method: curation
TSC
Allele origin: germline
Tuberous sclerosis database (TSC1)
Accession: SCV000083195.2
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
Functional assessment of TSC1 missense variants identified in individuals with tuberous sclerosis complex. Hoogeveen-Westerveld M Human mutation 2012 PMID: 22161988

Text-mined citations for rs397514840...

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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