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TSC2 tuberous sclerosis 2 [ Homo sapiens (human) ]

Gene ID: 7249, updated on 13-May-2016
Official Symbol
TSC2provided by HGNC
Official Full Name
tuberous sclerosis 2provided by HGNC
Primary source
HGNC: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]
Orthologs
Location:
16p13.3
Exon count:
42
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 16 NC_000016.10 (2047936..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 SLC9A3 regulator 2 Neighboring gene nth-like DNA glycosylase 1 Neighboring gene uncharacterized LOC105371049 Neighboring gene microRNA 1225 Neighboring gene polycystin 1, transient receptor potential channel interacting

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)

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
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
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
 
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 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
 
positive chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of GTPase activity 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
 
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, OTTHUMP00000158940, ENST00000219476, OTTHUMT00000250657
    Conserved Domains (3) summary
    pfam02145
    Location:15611750
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Tuberin; Tuberin
    pfam11864
    Location:51472
    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, OTTHUMP00000198394, ENST00000401874, OTTHUMT00000319841
    Conserved Domains (3) summary
    pfam02145
    Location:14941683
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Tuberin; Tuberin
    pfam11864
    Location:51472
    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, OTTHUMP00000198395, ENST00000350773, OTTHUMT00000319842
    Conserved Domains (3) summary
    pfam02145
    Location:15381727
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Tuberin; Tuberin
    pfam11864
    Location:51472
    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
    UniProtKB/Swiss-Prot
    P49815
    Conserved Domains (3) summary
    pfam02145
    Location:14581647
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:520867
    Tuberin; Tuberin
    pfam11864
    Location:51435
    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
    UniProtKB/Swiss-Prot
    P49815
    UniProtKB/TrEMBL
    B3KWH7
    Conserved Domains (3) summary
    pfam02145
    Location:14461635
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:508855
    Tuberin; Tuberin
    pfam11864
    Location:2423
    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:13171506
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:357704
    Tuberin; Tuberin
    pfam11864
    Location:1272
    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
    UniProtKB/Swiss-Prot
    P49815
    UniProtKB/TrEMBL
    H3BMQ0
    Conserved Domains (3) summary
    pfam02145
    Location:15051694
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:568915
    Tuberin; Tuberin
    pfam11864
    Location:62483
    DUF3384; Domain of unknown function (DUF3384)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p2 Primary Assembly

    Range
    2047936..2088712
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522638.1XP_011520940.1  

    Conserved Domains (3) summary
    pfam02145
    Location:15421731
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:520867
    Tuberin; Tuberin
    pfam11864
    Location:51435
    DUF3384; Domain of unknown function (DUF3384)
  2. XM_011522641.1XP_011520943.1  

    Related
    ENSP00000399232, OTTHUMP00000255506, ENST00000439673, OTTHUMT00000434564
    Conserved Domains (3) summary
    pfam02145
    Location:14581647
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:520867
    Tuberin; Tuberin
    pfam11864
    Location:51435
    DUF3384; Domain of unknown function (DUF3384)
  3. XM_011522636.1XP_011520938.1  

    Conserved Domains (3) summary
    pfam02145
    Location:15791768
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Tuberin; Tuberin
    pfam11864
    Location:51472
    DUF3384; Domain of unknown function (DUF3384)
  4. XM_011522637.1XP_011520939.1  

    Conserved Domains (3) summary
    pfam02145
    Location:15781767
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Tuberin; Tuberin
    pfam11864
    Location:51472
    DUF3384; Domain of unknown function (DUF3384)
  5. XM_011522639.1XP_011520941.1  

    Conserved Domains (3) summary
    pfam02145
    Location:15361725
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Tuberin; Tuberin
    pfam11864
    Location:51472
    DUF3384; Domain of unknown function (DUF3384)
  6. XM_005255529.3XP_005255586.2  

    See identical proteins and their annotated locations for XP_005255586.2

    UniProtKB/Swiss-Prot
    P49815
    Conserved Domains (3) summary
    pfam02145
    Location:15181707
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Tuberin; Tuberin
    pfam11864
    Location:51472
    DUF3384; Domain of unknown function (DUF3384)
  7. XM_005255531.3XP_005255588.2  

    See identical proteins and their annotated locations for XP_005255588.2

    UniProtKB/TrEMBL
    X5D2U8
    Related
    ENSP00000371978, OTTHUMP00000198397, ENST00000382538, OTTHUMT00000319845
    Conserved Domains (3) summary
    pfam02145
    Location:14951684
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Tuberin; Tuberin
    pfam11864
    Location:51472
    DUF3384; Domain of unknown function (DUF3384)
  8. XM_011522640.1XP_011520942.1  

    Conserved Domains (3) summary
    pfam02145
    Location:15351724
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:557904
    Tuberin; Tuberin
    pfam11864
    Location:51472
    DUF3384; Domain of unknown function (DUF3384)

Alternate CHM1_1.1

Genomic

  1. NC_018927.2 Alternate CHM1_1.1

    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.