Format

Send to:

Choose Destination

TSC2 TSC complex subunit 2 [ Homo sapiens (human) ]

Gene ID: 7249, updated on 29-Nov-2020

Summary

Official Symbol
TSC2provided by HGNC
Official Full Name
TSC complex subunit 2provided by HGNC
Primary source
HGNC:HGNC:12363
See related
Ensembl:ENSG00000103197 MIM:191092
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]
Expression
Ubiquitous expression in testis (RPKM 18.9), thyroid (RPKM 12.5) and 25 other tissues See more
Orthologs

Genomic context

See TSC2 in Genome Data Viewer
Location:
16p13.3
Exon count:
44
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (2047804..2089491)
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 CRISPRi-validated cis-regulatory element chr16.496 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

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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 type II
MedGen: C1846385 OMIM: 607341 GeneReviews: Not available
Compare labs
Joint influence of small-effect genetic variants on human longevity.
GeneReviews: Not available
Lymphangiomyomatosis
MedGen: C0751674 OMIM: 606690 GeneReviews: Not available
Compare labs
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
GeneReviews: Not available
Tuberous sclerosis 2
MedGen: C1860707 OMIM: 613254 GeneReviews: Tuberous Sclerosis Complex
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2020-06-10)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2020-06-10)

ClinGen Genome Curation PagePubMed

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ43106

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
GTPase activator activity IDA
Inferred from Direct Assay
more info
PubMed 
Hsp90 protein binding IPI
Inferred from Physical Interaction
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 
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
PubMed 
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
PubMed 
negative regulation of cell population 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
PubMed 
negative regulation of mitophagy 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
PubMed 
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
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
TSC1-TSC2 complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
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 
postsynaptic density EXP
Inferred from Experiment
more info
PubMed 
postsynaptic density IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
tuberin
Names
protein phosphatase 1, regulatory subunit 160
tuberous sclerosis 2 protein

NCBI Reference Sequences (RefSeq)

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_000548.5NP_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)
    AC093513, AK295672, AK299343, CA427637, DC402106, X75621
    Consensus CDS
    CCDS10458.1
    UniProtKB/Swiss-Prot
    P49815
    Related
    ENSP00000219476.3, ENST00000219476.9
    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_001077183.3NP_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, AC093513, CA427637, DC402106
    Consensus CDS
    CCDS58408.1
    UniProtKB/Swiss-Prot
    P49815
    UniProtKB/TrEMBL
    X5D7Q2
    Related
    ENSP00000384468.2, ENST00000401874.7
    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_001114382.3NP_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)
    AC093513, AK295672, BC150300, CA427637, DC402106
    Consensus CDS
    CCDS45384.1
    UniProtKB/Swiss-Prot
    P49815
    Related
    ENSP00000344383.4, ENST00000350773.9
    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_001318827.2NP_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)
    AC093513, AK295672, AK299343, CA427637, DC402106
    Consensus CDS
    CCDS81933.1
    UniProtKB/Swiss-Prot
    P49815
    Related
    ENSP00000399232.2, ENST00000439673.6
    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_001318829.2NP_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)
    AC093513, AK125096, AK295672, CA427637, DC402106
    Consensus CDS
    CCDS81934.1
    UniProtKB/Swiss-Prot
    P49815
    UniProtKB/TrEMBL
    B3KWH7
    Related
    ENSP00000371978.6, ENST00000382538.10
    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_001318831.2NP_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)
    AC093513, 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_001318832.2NP_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)
    AC093513, AK295672, AK295728, CA427637
    Consensus CDS
    CCDS81932.1
    UniProtKB/Swiss-Prot
    P49815
    UniProtKB/TrEMBL
    H3BMQ0
    Related
    ENSP00000454487.1, ENST00000568454.6
    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)
  8. NM_001363528.2NP_001350457.1  tuberin isoform 10

    Status: REVIEWED

    Source sequence(s)
    AC093513, KJ534954
    Related
    ENSP00000493846.1, ENST00000642797.1
    Conserved Domains (3) summary
    pfam02145
    Location:14961682
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:555903
    Tuberin; Tuberin
    pfam11864
    Location:55469
    DUF3384; Domain of unknown function (DUF3384)
  9. NM_001370404.1NP_001357333.1  tuberin isoform 11

    Status: REVIEWED

    Source sequence(s)
    AC093513
    Related
    ENSP00000494514.1, ENST00000642936.1
    Conserved Domains (3) summary
    pfam02145
    Location:15181704
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:555903
    Tuberin
    pfam11864
    Location:54469
    DUF3384; Domain of unknown function (DUF3384)
  10. NM_001370405.1NP_001357334.1  tuberin isoform 12

    Status: REVIEWED

    Source sequence(s)
    AC093513
    Related
    ENSP00000495099.1, ENST00000642561.1
    Conserved Domains (3) summary
    pfam02145
    Location:15191701
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:555903
    Tuberin
    pfam11864
    Location:54469
    DUF3384; Domain of unknown function (DUF3384)
  11. NM_021055.3NP_066399.2  tuberin isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC093513, CA427637
    Consensus CDS
    CCDS10459.1
    Related
    ENSP00000496262.1, ENST00000644043.1
    Conserved Domains (3) summary
    pfam02145
    Location:15191705
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:555903
    Tuberin; Tuberin
    pfam11864
    Location:55469
    DUF3384; Domain of unknown function (DUF3384)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    2047804..2089491
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522638.2XP_011520940.2  tuberin isoform X4

  2. XM_017023618.1XP_016879107.1  tuberin isoform X12

    Related
    ENSP00000495459.1, ENST00000642365.1
  3. 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)
  4. 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)
  5. XM_017023615.1XP_016879104.1  tuberin isoform X3

    Related
    ENSP00000495921.1, ENST00000646388.1
  6. XM_011522639.2XP_011520941.1  tuberin isoform X5

    Related
    ENSP00000496317.1, ENST00000644335.1
    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)
  7. 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)
  8. XM_024450413.1XP_024306181.1  tuberin isoform X7

    Related
    ENSP00000496611.1, ENST00000644329.1
    Conserved Domains (3) summary
    pfam02145
    Location:14951655
    Rap_GAP; Rap/ran-GAP
    pfam03542
    Location:555903
    Tuberin
    pfam11864
    Location:55469
    DUF3384; Domain of unknown function (DUF3384)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. 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.
Support Center