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TSC2 tuberous sclerosis 2 [ Homo sapiens (human) ]

Gene ID: 7249, updated on 19-Jul-2014
Official Symbol
TSC2provided by HGNC
Official Full Name
tuberous sclerosis 2provided by HGNC
Primary source
HGNC:12363
See related
Ensembl:ENSG00000103197; HPRD:01850; MIM:191092; Vega:OTTHUMG00000128745
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LAM; TSC4; PPP1R160
Summary
Mutations in this gene lead to tuberous sclerosis complex. Its gene product is believed to be a tumor suppressor and is able to stimulate specific GTPases. The protein associates with hamartin in a cytosolic complex, possibly acting as a chaperone for hamartin. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
See TSC2 in Epigenomics, MapViewer
Location:
16p13.3
Exon count:
42
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 16 NC_000016.10 (2047802..2088712)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (2097472..2138713)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 2 Neighboring gene neuropeptide W Neighboring gene nth endonuclease III-like 1 (E. coli) Neighboring gene microRNA 1225 Neighboring gene polycystic kidney disease 1 (autosomal dominant) Neighboring gene microRNA 6511b-1

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Professional guidelines

Description
Professional guideline
ACMG 2013

The ACMG recommends that laboratories performing clinical sequencing seek and report mutations in TSC2 that are pathogenic or expected to be pathogenic.

GuidelinePubMed

Associated conditions

Description Tests
Lymphangiomyomatosis
MedGen: C0751674 OMIM: 606690 GeneReviews: Not available
Compare labs
Tuberous sclerosis 2
MedGen: C1860707 OMIM: 613254 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-02-22)

ISCA Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-02-22)

ISCA Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Joint influence of small-effect genetic variants on human longevity.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog
  • AKT phosphorylates targets in the cytosol, organism-specific biosystem (from REACTOME)
    AKT phosphorylates targets in the cytosol, organism-specific biosystemFollowing activation, AKT can phosphorylate an array of target proteins in the cytoplasm, many of which are involved in cell survival control. Phosphorylation of TSC2 feeds positively to the TOR kina...
  • AMPK signaling, organism-specific biosystem (from WikiPathways)
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  • AMPK signaling pathway, organism-specific biosystem (from KEGG)
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  • AMPK signaling pathway, conserved biosystem (from KEGG)
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    Direct p53 effectors, organism-specific biosystem
    Direct p53 effectors
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    Downstream signaling of activated FGFR, organism-specific biosystemSignaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that be...
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    Energy dependent regulation of mTOR by LKB1-AMPK, organism-specific biosystemUpon formation of a trimeric LKB1:STRAD:MO25 complex, LKB1 phosphorylates and activates AMPK. If the AMP:ATP ratio rises, this activation is maintained and AMPK activates the TSC complex by phosphory...
  • FSH signaling pathway, organism-specific biosystem (from WikiPathways)
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    Fc epsilon receptor (FCERI) signaling, organism-specific biosystemMast cells (MC) are distributed in tissues throughout the human body and have long been recognized as key cells of type I hypersensitivity reactions. They also play important roles in inflammatory an...
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  • IRS-related events, organism-specific biosystem (from REACTOME)
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  • Integrated Breast Cancer Pathway, organism-specific biosystem (from WikiPathways)
    Integrated Breast Cancer Pathway, organism-specific biosystemThis pathway incorporates the most important proteins for Breast Cancer. The Rp score from the Connectivity-Maps (C-Maps) webserver was used to determine the rank of the most important proteins in Br...
  • LKB1 signaling events, organism-specific biosystem (from Pathway Interaction Database)
    LKB1 signaling events, organism-specific biosystem
    LKB1 signaling events
  • Monoamine Transport, organism-specific biosystem (from WikiPathways)
    Monoamine Transport, organism-specific biosystem
    Monoamine Transport
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    PI3K Cascade, organism-specific biosystem
    PI3K Cascade
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    PI3K events in ERBB2 signaling, organism-specific biosystemERBB2:ERBB3 and ERBB2:ERBB4cyt1 heterodimers activate PI3K signaling by direct binding of PI3K regulatory subunit p85 (Yang et al. 2007, Cohen et al. 1996, Kaushansky et al. 2008) to phosphorylated t...
  • PI3K events in ERBB4 signaling, organism-specific biosystem (from REACTOME)
    PI3K events in ERBB4 signaling, organism-specific biosystemThe CYT1 isoforms of ERBB4 possess a C-tail tyrosine residue that, upon trans-autophosphorylation, serves as a docking site for the p85 alpha subunit of PI3K - PIK3R1 (Kaushansky et al. 2008, Cohen e...
  • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
    PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
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  • PKB-mediated events, organism-specific biosystem (from REACTOME)
    PKB-mediated events, organism-specific biosystemPKB and PDK1 are activated via membrane-bound PIP3. Activated PDK1 phosphorylates PKB, which in turn phosphorylates PDE3B. The latter hydrolyses cAMP to 5'AMP, depleting cAMP pools.
  • Prostate Cancer, organism-specific biosystem (from WikiPathways)
    Prostate Cancer, organism-specific biosystem
    Prostate Cancer
  • Regulation of Rheb GTPase activity by AMPK, organism-specific biosystem (from REACTOME)
    Regulation of Rheb GTPase activity by AMPK, organism-specific biosystemActivated AMPK phosphorylates TSC2 and activates the TSC complex. TSC2 functions as a GTPase-activating protein and stimulates the intrinsic GTPase activity of a small G-protein Rheb. This results in...
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  • Validated targets of C-MYC transcriptional repression, organism-specific biosystem (from Pathway Interaction Database)
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    Validated targets of C-MYC transcriptional repression
  • mTOR signaling pathway, organism-specific biosystem (from KEGG)
    mTOR signaling pathway, organism-specific biosystem
    mTOR signaling pathway
  • mTOR signaling pathway, organism-specific biosystem (from Pathway Interaction Database)
    mTOR signaling pathway, organism-specific biosystem
    mTOR signaling pathway
  • mTOR signaling pathway, conserved biosystem (from KEGG)
    mTOR signaling pathway, conserved biosystem
    mTOR signaling pathway
  • mTOR signalling, organism-specific biosystem (from REACTOME)
    mTOR signalling, organism-specific biosystem
    mTOR signalling
  • p38 signaling mediated by MAPKAP kinases, organism-specific biosystem (from Pathway Interaction Database)
    p38 signaling mediated by MAPKAP kinases, organism-specific biosystem
    p38 signaling mediated by MAPKAP kinases
  • p53 signaling pathway, organism-specific biosystem (from KEGG)
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  • p53 signaling pathway, conserved biosystem (from KEGG)
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Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ43106

Gene Ontology Provided by GOA

Function Evidence Code Pubs
14-3-3 protein binding IEA
Inferred from Electronic Annotation
more info
 
GTPase activator activity IDA
Inferred from Direct Assay
more info
PubMed 
phosphatase binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Fc-epsilon receptor signaling pathway TAS
Traceable Author Statement
more info
 
acute-phase response IEA
Inferred from Electronic Annotation
more info
 
cell cycle arrest TAS
Traceable Author Statement
more info
 
cell projection organization IEA
Inferred from Electronic Annotation
more info
 
endocytosis TAS
Traceable Author Statement
more info
PubMed 
epidermal growth factor receptor signaling pathway TAS
Traceable Author Statement
more info
 
fibroblast growth factor receptor signaling pathway TAS
Traceable Author Statement
more info
 
heart development ISS
Inferred from Sequence or Structural Similarity
more info
 
innate immune response TAS
Traceable Author Statement
more info
 
insulin receptor signaling pathway TAS
Traceable Author Statement
more info
 
insulin-like growth factor receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of MAP kinase activity IEA
Inferred from Electronic Annotation
more info
 
negative regulation of TOR signaling IBA
Inferred from Biological aspect of Ancestor
more info
 
negative regulation of Wnt signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
negative regulation of cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of cell size IEA
Inferred from Electronic Annotation
more info
 
negative regulation of epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of insulin receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
negative regulation of phosphatidylinositol 3-kinase signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of protein kinase B signaling IBA
Inferred from Biological aspect of Ancestor
more info
 
negative regulation of protein kinase B signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of protein kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
neural tube closure ISS
Inferred from Sequence or Structural Similarity
more info
 
neurotrophin TRK receptor signaling pathway TAS
Traceable Author Statement
more info
 
phosphatidylinositol 3-kinase signaling IEA
Inferred from Electronic Annotation
more info
 
phosphatidylinositol-mediated signaling TAS
Traceable Author Statement
more info
 
positive chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of Ras GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
protein heterooligomerization IEA
Inferred from Electronic Annotation
more info
 
protein homooligomerization IEA
Inferred from Electronic Annotation
more info
 
protein import into nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
protein kinase B signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
protein localization ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell cycle IBA
Inferred from Biological aspect of Ancestor
more info
 
regulation of endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of insulin receptor signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
vesicle-mediated transport TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
NOT Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
TSC1-TSC2 complex IDA
Inferred from Direct Assay
more info
PubMed 
caveola IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
 
colocalizes_with cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
dendrite IEA
Inferred from Electronic Annotation
more info
 
growth cone IEA
Inferred from Electronic Annotation
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
NOT nucleus IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
tuberin
Names
tuberin
tuberous sclerosis 2 protein
protein phosphatase 1, regulatory subunit 160

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_005895.1 

    Range
    3684..44407
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_487

mRNA and Protein(s)

  1. NM_000548.3NP_000539.2  tuberin isoform 1

    See proteins identical to NP_000539.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB210000, BM966762, X75621
    Consensus CDS
    CCDS10458.1
    UniProtKB/Swiss-Prot
    P49815
    Related
    ENSP00000219476, OTTHUMP00000158940, ENST00000219476, OTTHUMT00000250657
    Conserved Domains (3) summary
    pfam02145
    Location:15611750
    Blast Score: 455
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Blast Score: 1339
    Tuberin; Tuberin
    pfam11864
    Location:51472
    Blast Score: 1080
    DUF3384; Domain of unknown function (DUF3384)
  2. NM_001077183.1NP_001070651.1  tuberin isoform 4

    See proteins identical to NP_001070651.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in multiple places compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AB210000, BM966762
    Consensus CDS
    CCDS58408.1
    UniProtKB/Swiss-Prot
    P49815
    UniProtKB/TrEMBL
    X5D7Q2
    Related
    ENSP00000384468, OTTHUMP00000198394, ENST00000401874, OTTHUMT00000319841
    Conserved Domains (3) summary
    pfam02145
    Location:14941683
    Blast Score: 455
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Blast Score: 1339
    Tuberin; Tuberin
    pfam11864
    Location:51472
    Blast Score: 1081
    DUF3384; Domain of unknown function (DUF3384)
  3. NM_001114382.1NP_001107854.1  tuberin isoform 5

    See proteins identical to NP_001107854.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 5), compared to isoform 1.
    Source sequence(s)
    BC025364, BC150300, BF194994, DA316794, DB288276
    Consensus CDS
    CCDS45384.1
    UniProtKB/Swiss-Prot
    P49815
    Related
    ENSP00000344383, OTTHUMP00000198395, ENST00000350773, OTTHUMT00000319842
    Conserved Domains (3) summary
    pfam02145
    Location:15381727
    Blast Score: 455
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Blast Score: 1340
    Tuberin; Tuberin
    pfam11864
    Location:51472
    Blast Score: 1080
    DUF3384; Domain of unknown function (DUF3384)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000016.10 

    Range
    2047802..2088712
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005255527.2XP_005255584.1  

    Conserved Domains (3) summary
    pfam02145
    Location:16521841
    Blast Score: 455
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:648995
    Blast Score: 1346
    Tuberin; Tuberin
    pfam11864
    Location:142563
    Blast Score: 1088
    DUF3384; Domain of unknown function (DUF3384)
  2. XM_005255528.2XP_005255585.1  

    See proteins identical to XP_005255585.1

    Conserved Domains (3) summary
    pfam02145
    Location:16291818
    Blast Score: 455
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:648995
    Blast Score: 1346
    Tuberin; Tuberin
    pfam11864
    Location:142563
    Blast Score: 1089
    DUF3384; Domain of unknown function (DUF3384)
  3. XM_005255529.2XP_005255586.1  

    Conserved Domains (3) summary
    pfam02145
    Location:16091798
    Blast Score: 455
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:648995
    Blast Score: 1345
    Tuberin; Tuberin
    pfam11864
    Location:142563
    Blast Score: 1088
    DUF3384; Domain of unknown function (DUF3384)
  4. XM_005255531.2XP_005255588.1  

    Conserved Domains (3) summary
    pfam02145
    Location:15861775
    Blast Score: 455
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:648995
    Blast Score: 1345
    Tuberin; Tuberin
    pfam11864
    Location:142563
    Blast Score: 1089
    DUF3384; Domain of unknown function (DUF3384)
  5. XM_005255530.2XP_005255587.1  

    Conserved Domains (3) summary
    pfam02145
    Location:16081797
    Blast Score: 455
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:648995
    Blast Score: 1345
    Tuberin; Tuberin
    pfam11864
    Location:142563
    Blast Score: 1089
    DUF3384; Domain of unknown function (DUF3384)
  6. XM_005255532.2XP_005255589.1  

    Conserved Domains (3) summary
    pfam02145
    Location:15851774
    Blast Score: 455
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:648995
    Blast Score: 1345
    Tuberin; Tuberin
    pfam11864
    Location:142563
    Blast Score: 1089
    DUF3384; Domain of unknown function (DUF3384)

Alternate HuRef

Genomic

  1. AC_000148.1 

    Range
    2022255..2063441
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018927.2 

    Range
    2097965..2138628
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_021055.1: Suppressed sequence

    Description
    NM_021055.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
  2. NM_021056.1: Suppressed sequence

    Description
    NM_021056.1: This RefSeq was temporarily suppressed because currently there is insufficient support for the transcript and the protein.