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    TSC2 tuberous sclerosis 2 [ Homo sapiens (human) ]

    Gene ID: 7249, updated on 25-May-2017
    Official Symbol
    TSC2provided by HGNC
    Official Full Name
    tuberous sclerosis 2provided by HGNC
    Primary source
    HGNC:HGNC:12363
    See related
    Ensembl:ENSG00000103197 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]
    Orthologs
    Location:
    16p13.3
    Exon count:
    44
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 16 NC_000016.10 (2047804..2088720)
    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 SLC9A3 regulator 2 Neighboring gene neuropeptide W Neighboring gene nth like DNA glycosylase 1 Neighboring gene uncharacterized LOC105371049 Neighboring gene microRNA 1225 Neighboring gene polycystin 1, transient receptor potential channel interacting

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    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
    Focal cortical dysplasia of Taylor
    MedGen: C1846385 OMIM: 607341 GeneReviews: Not available
    Compare labs
    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)

    ClinGen Genome Curation Page
    Haploinsufficency

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

    ClinGen 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
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    • Brain-Derived Neurotrophic Factor (BDNF) signaling pathway, organism-specific biosystem (from WikiPathways)
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      mTOR signaling pathway, organism-specific biosystem
      mTOR signaling pathway
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      p38 signaling mediated by MAPKAP kinases, organism-specific biosystem
      p38 signaling mediated by MAPKAP kinases
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      p53 signaling pathway, conserved biosystemp53 activation is induced by a number of stress signals, including DNA damage, oxidative stress and activated oncogenes. The p53 protein is employed as a transcriptional activator of p53-regulated ge...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ43106

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    small GTPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    anoikis IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    cell cycle arrest TAS
    Traceable Author Statement
    more info
     
    endocytosis TAS
    Traceable Author Statement
    more info
    PubMed 
    heart development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    insulin-like growth factor receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    membrane organization TAS
    Traceable Author Statement
    more info
     
    negative regulation of TOR signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    negative regulation of TOR signaling IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    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 insulin receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    negative regulation of macromitophagy NAS
    Non-traceable Author Statement
    more info
    PubMed 
    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
     
    positive chemotaxis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of GTPase activity IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of macroautophagy IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    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
     
    regulation of small GTPase mediated signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    vesicle-mediated transport TAS
    Traceable Author Statement
    more info
    PubMed 
    viral process IEA
    Inferred from Electronic Annotation
    more info
     
    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 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
    protein phosphatase 1, regulatory subunit 160
    tuberous sclerosis 2 protein

    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 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_000548.4NP_000539.2  tuberin isoform 1

      See identical proteins and their annotated locations for NP_000539.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK295672, AK299343, CA427637, DC402106, X75621
      Consensus CDS
      CCDS10458.1
      UniProtKB/Swiss-Prot
      P49815
      Related
      ENSP00000219476.3, OTTHUMP00000158940, ENST00000219476.7, OTTHUMT00000250657
      Conserved Domains (3) summary
      pfam02145
      Location:15621748
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:555903
      Tuberin; Tuberin
      pfam11864
      Location:54466
      DUF3384; Domain of unknown function (DUF3384)
    2. NM_001077183.2NP_001070651.1  tuberin isoform 4

      See identical proteins and their annotated locations for 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, CA427637, DC402106
      Consensus CDS
      CCDS58408.1
      UniProtKB/Swiss-Prot
      P49815
      UniProtKB/TrEMBL
      X5D7Q2
      Related
      ENSP00000384468.2, OTTHUMP00000198394, ENST00000401874.6, OTTHUMT00000319841
      Conserved Domains (3) summary
      pfam02145
      Location:14951681
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:555903
      Tuberin; Tuberin
      pfam11864
      Location:54466
      DUF3384; Domain of unknown function (DUF3384)
    3. NM_001114382.2NP_001107854.1  tuberin isoform 5

      See identical proteins and their annotated locations for NP_001107854.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. It encodes isoform 5, which is shorter than isoform 1.
      Source sequence(s)
      AK295672, BC150300, CA427637, DC402106
      Consensus CDS
      CCDS45384.1
      UniProtKB/Swiss-Prot
      P49815
      Related
      ENSP00000344383.4, OTTHUMP00000198395, ENST00000350773.8, OTTHUMT00000319842
      Conserved Domains (3) summary
      pfam02145
      Location:15391725
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:555903
      Tuberin; Tuberin
      pfam11864
      Location:54466
      DUF3384; Domain of unknown function (DUF3384)
    4. NM_001318827.1NP_001305756.1  tuberin isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks three alternate in-frame exons in the coding region, compared to variant 1. It encodes isoform 6, which lacks three separate internal in-frame segments and is shorter, compared to isoform 1.
      Source sequence(s)
      AK295672, AK299343, CA427637, DC402106
      Consensus CDS
      CCDS81933.1
      UniProtKB/Swiss-Prot
      P49815
      Related
      ENSP00000399232.2, OTTHUMP00000255506, ENST00000439673.6, OTTHUMT00000434564
      Conserved Domains (3) summary
      pfam02145
      Location:14591645
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:518866
      Tuberin; Tuberin
      pfam11864
      Location:77429
      DUF3384; Domain of unknown function (DUF3384)
    5. NM_001318829.1NP_001305758.1  tuberin isoform 7

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR, uses a downstream start codon and contains multiple coding region differences, compared to variant 1. It encodes isoform 7, which is shorter than isoform 1.
      Source sequence(s)
      AK125096, AK295672, CA427637, DC402106
      Consensus CDS
      CCDS81934.1
      UniProtKB/Swiss-Prot
      P49815
      UniProtKB/TrEMBL
      B3KWH7
      Related
      ENSP00000371978.6, OTTHUMP00000198397, ENST00000382538.10, OTTHUMT00000319845
      Conserved Domains (3) summary
      pfam02145
      Location:14471633
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:506854
      Tuberin; Tuberin
      pfam11864
      Location:5417
      DUF3384; Domain of unknown function (DUF3384)
    6. NM_001318831.1NP_001305760.1  tuberin isoform 8

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR, uses a downstream start codon and contains multiple coding region differences, compared to variant 1. It encodes isoform 8, which is shorter than isoform 1.
      Source sequence(s)
      AK295672, AK299343, BX647816, CA427637, DC402106
      UniProtKB/Swiss-Prot
      P49815
      UniProtKB/TrEMBL
      Q5HYF7
      Conserved Domains (3) summary
      pfam02145
      Location:13181504
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:355703
      Tuberin; Tuberin
      pfam11864
      Location:1266
      DUF3384; Domain of unknown function (DUF3384)
    7. NM_001318832.1NP_001305761.1  tuberin isoform 9

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) differs in the 5' UTR, uses an alternate start codon and contains multiple coding region differences, compared to variant 1. It encodes isoform 9, which is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK295672, AK295728, CA427637
      Consensus CDS
      CCDS81932.1
      UniProtKB/Swiss-Prot
      P49815
      UniProtKB/TrEMBL
      H3BMQ0
      Related
      ENSP00000454487.1, OTTHUMP00000198396, ENST00000568454.5, OTTHUMT00000319844
      Conserved Domains (3) summary
      pfam02145
      Location:15061692
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:566914
      Tuberin; Tuberin
      pfam11864
      Location:65477
      DUF3384; Domain of unknown function (DUF3384)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p7 Primary Assembly

      Range
      2047804..2088720
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011522638.2XP_011520940.2  tuberin isoform X4

    2. XM_017023617.1XP_016879106.1  tuberin isoform X10

    3. XM_017023618.1XP_016879107.1  tuberin isoform X11

    4. XM_011522636.2XP_011520938.1  tuberin isoform X1

      Conserved Domains (3) summary
      pfam02145
      Location:15801766
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:555903
      Tuberin; Tuberin
      pfam11864
      Location:54466
      DUF3384; Domain of unknown function (DUF3384)
    5. XM_011522637.2XP_011520939.1  tuberin isoform X2

      Conserved Domains (3) summary
      pfam02145
      Location:15791765
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:555903
      Tuberin; Tuberin
      pfam11864
      Location:54466
      DUF3384; Domain of unknown function (DUF3384)
    6. XM_017023615.1XP_016879104.1  tuberin isoform X3

    7. XM_011522639.2XP_011520941.1  tuberin isoform X5

      Conserved Domains (3) summary
      pfam02145
      Location:15371723
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:555903
      Tuberin; Tuberin
      pfam11864
      Location:54466
      DUF3384; Domain of unknown function (DUF3384)
    8. XM_005255529.4XP_005255586.2  tuberin isoform X7

      See identical proteins and their annotated locations for XP_005255586.2

      UniProtKB/Swiss-Prot
      P49815
      Conserved Domains (3) summary
      pfam02145
      Location:15191705
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:555903
      Tuberin; Tuberin
      pfam11864
      Location:54466
      DUF3384; Domain of unknown function (DUF3384)
    9. XM_005255531.4XP_005255588.2  tuberin isoform X9

      See identical proteins and their annotated locations for XP_005255588.2

      UniProtKB/TrEMBL
      X5D2U8
      Conserved Domains (3) summary
      pfam02145
      Location:14961682
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:555903
      Tuberin; Tuberin
      pfam11864
      Location:54466
      DUF3384; Domain of unknown function (DUF3384)
    10. XM_011522640.2XP_011520942.1  tuberin isoform X6

      Conserved Domains (3) summary
      pfam02145
      Location:15361722
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:555903
      Tuberin; Tuberin
      pfam11864
      Location:54466
      DUF3384; Domain of unknown function (DUF3384)
    11. XM_017023616.1XP_016879105.1  tuberin isoform X8

      UniProtKB/Swiss-Prot
      P49815
      Conserved Domains (3) summary
      pfam02145
      Location:15181704
      Rap_GAP; Rap/ran-GAP
      pfam03542
      Location:555903
      Tuberin; Tuberin
      pfam11864
      Location:54466
      DUF3384; Domain of unknown function (DUF3384)

    Alternate CHM1_1.1

    Genomic

    1. NC_018927.2 Alternate CHM1_1.1

      Range
      2097871..2138636
      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.
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