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NM_000548.5(TSC2):c.2666C>T (p.Ala889Val)

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Interpretation:
Conflicting interpretations of pathogenicity​

Pathogenic(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Apr 2, 2018)
Last evaluated:
Oct 19, 2017
Accession:
VCV000049586.2
Variation ID:
49586
Description:
single nucleotide variant
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NM_000548.5(TSC2):c.2666C>T (p.Ala889Val)

Allele ID
58748
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p13.3
Genomic location
16: 2076094 (GRCh38) GRCh38 UCSC
16: 2126095 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_487t1:c.2666C>T
NC_000016.10:g.2076094C>T
NC_000016.9:g.2126095C>T
... more HGVS
Protein change
A889V, A689V, A840V, A852V, A900V
Other names
-
Canonical SPDI
NC_000016.10:2076093:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA017841
Tuberous sclerosis database (TSC2): TSC2_01111
dbSNP: rs137854155
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Oct 19, 2017 RCV000201152.1
not provided 1 no assertion provided - RCV000042847.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TSC2 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
6463 6629

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jul 05, 2012)
criteria provided, single submitter
Method: clinical testing
Tuberous sclerosis 2
(Autosomal dominant inheritance)
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000255887.2
Submitted: (Oct 06, 2015)
Evidence details
Publications
PubMed (1)
Uncertain significance
(Oct 19, 2017)
criteria provided, single submitter
Method: clinical testing
Tuberous sclerosis 2
Allele origin: germline
Invitae
Accession: SCV000765936.1
Submitted: (Apr 02, 2018)
Evidence details
Publications
PubMed (3)
Comment:
This sequence change replaces alanine with valine at codon 889 of the TSC2 protein (p.Ala889Val). The alanine residue is highly conserved and there is a … (more)
not provided
(-)
no assertion provided
Method: curation
TSC
Allele origin: germline
Tuberous sclerosis database (TSC2)
Accession: SCV000066643.3
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 TSC2 variants identified in individuals with tuberous sclerosis complex. Hoogeveen-Westerveld M Human mutation 2013 PMID: 22903760
LOVD v.2.0: the next generation in gene variant databases. Fokkema IF Human mutation 2011 PMID: 21520333
Functional assessment of variants in the TSC1 and TSC2 genes identified in individuals with Tuberous Sclerosis Complex. Hoogeveen-Westerveld M Human mutation 2011 PMID: 21309039

Text-mined citations for rs137854155...

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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 24, 2021