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Aliases for TBC1D7 Gene

Aliases for TBC1D7 Gene

  • TBC1 Domain Family Member 7 2 3 3 5
  • Cell Migration-Inducing Protein 23 3 4
  • TS Complex Subunit 3 2 3
  • TBC7 3 4
  • TBC1 Domain Family, Member 7 2
  • MGCPH 3
  • PIG51 3

External Ids for TBC1D7 Gene

Previous GeneCards Identifiers for TBC1D7 Gene

  • GC06M013329
  • GC06M013374
  • GC06M013413
  • GC06M013305
  • GC06M013242

Summaries for TBC1D7 Gene

Entrez Gene Summary for TBC1D7 Gene

  • This gene encodes a member of the TBC-domain containing protein family. The encoded protein functions as a subunit of the tuberous sclerosis TSC1-TSC2 complex which plays a role in the regulation of cellular growth and differentiation. Mutations in this gene have been associated with autosomal recessive megalencephaly. Alternative splicing results in multiple transcript variants. Naturally occurring readthrough transcription occurs between this locus and downstream LOC100130357. [provided by RefSeq, Jan 2016]

GeneCards Summary for TBC1D7 Gene

TBC1D7 (TBC1 Domain Family Member 7) is a Protein Coding gene. Diseases associated with TBC1D7 include Macrocephaly/Megalencephaly Syndrome, Autosomal Recessive and Isolated Megalencephaly. Among its related pathways are Vesicle-mediated transport and mTOR signaling pathway (KEGG). Gene Ontology (GO) annotations related to this gene include GTPase activator activity and Rab GTPase binding.

UniProtKB/Swiss-Prot for TBC1D7 Gene

  • Component of the TSC-TBC complex, that contains TBC1D7 in addition to the TSC1-TSC2 complex and consists of the functional complex possessing GTPase-activating protein (GAP) activity toward RHEB in response to alterations in specific cellular growth conditions. The small GTPase RHEB is a direct activator of the protein kinase activity of mTORC1 and the TSC-TBC complex acts as a negative regulator of mTORC1 signaling cascade by acting as a GAP for RHEB. Participates in the proper sensing of growth factors and glucose, but not amino acids, by mTORC1. It is unclear whether TBC1D7 acts as a GTPase-activating protein and additional studies are required to answer this question.

Additional gene information for TBC1D7 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TBC1D7 Gene

Genomics for TBC1D7 Gene

GeneHancer (GH) Regulatory Elements for TBC1D7 Gene

Promoters and enhancers for TBC1D7 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J013327 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 677 +0.1 91 2.2 HDGF SMAD1 ARNT ARID4B SIN3A DMAP1 SLC30A9 POLR2B ZNF766 KLF13 TBC1D7 RPL15P3 SIRT5 GC06P013321 GC06P013319
GH06J013301 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 61.3 +25.1 25083 4.4 PKNOX1 FOXA2 SMAD1 SIN3A IRF4 FOS JUNB ZHX2 ZNF592 KAT8 TBC1D7 LOC100130357 ENSG00000272379 SIRT5 GFOD1 GC06P013319
GH06J013307 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 31.7 +20.8 20787 1.6 CAVIN1 CEBPB REST ZNF592 SP1 MEF2D SMARCA4 HMBOX1 ZNF24 ZBTB33 TBC1D7 ENSG00000272379 RNU1-11P GFOD1 GC06P013319 LOC100130357
GH06J013271 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 21.5 +54.3 54342 4.7 HDGF HNRNPUL1 PKNOX1 SMAD1 ARNT IRF4 POLR2B ZNF766 ZNF143 ZNF592 TBC1D7 RPL15P3 LOC100130357 SIRT5 ENSG00000272379 PHACTR1 PIR62166 LOC105374933
GH06J013258 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 21.1 +67.7 67651 4.3 HDGF PKNOX1 RB1 STAT5A BMI1 BATF KLF5 IRF4 ZNF207 ATF7 TBC1D7 RNU1-11P LOC100130357 PHACTR1 GFOD1 RANBP9 PIR62166 LOC105374933
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TBC1D7 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TBC1D7 gene promoter:

Genomic Locations for TBC1D7 Gene

Genomic Locations for TBC1D7 Gene
chr6:13,266,542-13,328,583
(GRCh38/hg38)
Size:
62,042 bases
Orientation:
Minus strand
chr6:13,266,774-13,328,815
(GRCh37/hg19)

Genomic View for TBC1D7 Gene

Genes around TBC1D7 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBC1D7 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBC1D7 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TBC1D7 Gene

Proteins for TBC1D7 Gene

  • Protein details for TBC1D7 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9P0N9-TBCD7_HUMAN
    Recommended name:
    TBC1 domain family member 7
    Protein Accession:
    Q9P0N9
    Secondary Accessions:
    • E7EV96
    • Q2TU37
    • Q53F44
    • Q5SZL7
    • Q86VM8
    • Q96MB8

    Protein attributes for TBC1D7 Gene

    Size:
    293 amino acids
    Molecular mass:
    33972 Da
    Quaternary structure:
    • Component of the TSC-TBC complex (also named Rhebulator complex), composed of the TSC1-TSC2 heterodimer and TBC1D7. Interacts with TSC1 (via C-terminal half of the coiled-coil domain).

    Three dimensional structures from OCA and Proteopedia for TBC1D7 Gene

    Alternative splice isoforms for TBC1D7 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBC1D7 Gene

Post-translational modifications for TBC1D7 Gene

  • Ubiquitination at posLast=277277, isoforms=2, 3, 4208, and isoforms=2, 3165
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TBC1D7 Gene

Domains & Families for TBC1D7 Gene

Gene Families for TBC1D7 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for TBC1D7 Gene

Suggested Antigen Peptide Sequences for TBC1D7 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with TBC1D7: view

No data available for UniProtKB/Swiss-Prot for TBC1D7 Gene

Function for TBC1D7 Gene

Molecular function for TBC1D7 Gene

UniProtKB/Swiss-Prot Function:
Component of the TSC-TBC complex, that contains TBC1D7 in addition to the TSC1-TSC2 complex and consists of the functional complex possessing GTPase-activating protein (GAP) activity toward RHEB in response to alterations in specific cellular growth conditions. The small GTPase RHEB is a direct activator of the protein kinase activity of mTORC1 and the TSC-TBC complex acts as a negative regulator of mTORC1 signaling cascade by acting as a GAP for RHEB. Participates in the proper sensing of growth factors and glucose, but not amino acids, by mTORC1. It is unclear whether TBC1D7 acts as a GTPase-activating protein and additional studies are required to answer this question.

Phenotypes From GWAS Catalog for TBC1D7 Gene

Gene Ontology (GO) - Molecular Function for TBC1D7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IDA 17646400
GO:0005515 protein binding IPI 17658474
GO:0017137 Rab GTPase binding IPI 17646400
genes like me logo Genes that share ontologies with TBC1D7: view
genes like me logo Genes that share phenotypes with TBC1D7: view

Animal Model Products

miRNA for TBC1D7 Gene

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TBC1D7 Gene

Localization for TBC1D7 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBC1D7 Gene

Cytoplasmic vesicle. Note=Localizes in the cytoplasmic vesicles of the endomembrane in association with TSC1-TSC2 complex.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TBC1D7 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
plasma membrane 1
extracellular 1
mitochondrion 1
peroxisome 1
nucleus 1
lysosome 1

Gene Ontology (GO) - Cellular Components for TBC1D7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0031410 cytoplasmic vesicle IDA,IEA 17658474
GO:0036064 ciliary basal body IDA 17646400
genes like me logo Genes that share ontologies with TBC1D7: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TBC1D7 Gene

Pathways & Interactions for TBC1D7 Gene

genes like me logo Genes that share pathways with TBC1D7: view

Pathways by source for TBC1D7 Gene

3 Reactome pathways for TBC1D7 Gene
1 KEGG pathway for TBC1D7 Gene
1 R&D Systems pathway for TBC1D7 Gene
1 Cell Signaling Technology pathway for TBC1D7 Gene

Gene Ontology (GO) - Biological Process for TBC1D7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031398 positive regulation of protein ubiquitination IDA 17658474
GO:0032007 negative regulation of TOR signaling IMP 22795129
GO:0043547 positive regulation of GTPase activity IDA 17646400
GO:0070848 response to growth factor IMP 22795129
GO:0090630 activation of GTPase activity IMP 22795129
genes like me logo Genes that share ontologies with TBC1D7: view

No data available for SIGNOR curated interactions for TBC1D7 Gene

Drugs & Compounds for TBC1D7 Gene

No Compound Related Data Available

Transcripts for TBC1D7 Gene

Unigene Clusters for TBC1D7 Gene

TBC1 domain family, member 7:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D7 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b · 9c ^ 10a · 10b · 10c ^ 11
SP1: - - - - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - -
SP4: - - - - - - - - - -
SP5: - - - - - -
SP6: - - - - - - - -
SP7: - - - - - - -
SP8: - - - - - - - -
SP9: - - -
SP10: - - - - - - -
SP11: - - - - -
SP12: - - - -
SP13: - - -
SP14: - - -
SP15: - - - - - - -

Relevant External Links for TBC1D7 Gene

GeneLoc Exon Structure for
TBC1D7
ECgene alternative splicing isoforms for
TBC1D7

Expression for TBC1D7 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TBC1D7 Gene

Protein differential expression in normal tissues from HIPED for TBC1D7 Gene

This gene is overexpressed in Fetal Brain (21.8), Frontal cortex (16.1), and Testis (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TBC1D7 Gene



Protein tissue co-expression partners for TBC1D7 Gene

NURSA nuclear receptor signaling pathways regulating expression of TBC1D7 Gene:

TBC1D7

SOURCE GeneReport for Unigene cluster for TBC1D7 Gene:

Hs.484678

mRNA Expression by UniProt/SwissProt for TBC1D7 Gene:

Q9P0N9-TBCD7_HUMAN
Tissue specificity: Highly expressed in heart, and slightly in kidney, liver and placenta.

Evidence on tissue expression from TISSUES for TBC1D7 Gene

  • Nervous system(4.4)
  • Kidney(4.3)
  • Blood(4.1)
  • Eye(4.1)
  • Skin(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TBC1D7 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • endocrine
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • chin
  • cranial nerve
  • eye
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • skull
  • tooth
Abdomen:
  • adrenal gland
General:
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with TBC1D7: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for TBC1D7 Gene

Orthologs for TBC1D7 Gene

This gene was present in the common ancestor of animals.

Orthologs for TBC1D7 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TBC1D7 34 33
  • 99.32 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TBC1D7 34 33
  • 90.44 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TBC1D7 34 33
  • 87.49 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TBC1D7 34
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TBC1D7 34
  • 86 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tbc1d7 33
  • 85.32 (n)
mouse
(Mus musculus)
Mammalia Tbc1d7 16 34 33
  • 84.76 (n)
chicken
(Gallus gallus)
Aves TBC1D7 34 33
  • 75.34 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TBC1D7 34
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tbc1d7 33
  • 72.49 (n)
Str.16760 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.20842 33
zebrafish
(Danio rerio)
Actinopterygii tbc1d7 34 33
  • 65.64 (n)
OneToOne
zgc73291 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002392 33
  • 47.6 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6182 34 33
  • 44.57 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 36 (a)
OneToOne
Species where no ortholog for TBC1D7 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TBC1D7 Gene

ENSEMBL:
Gene Tree for TBC1D7 (if available)
TreeFam:
Gene Tree for TBC1D7 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TBC1D7: view image

Paralogs for TBC1D7 Gene

(1) SIMAP similar genes for TBC1D7 Gene using alignment to 14 proteins:

  • TBCD7_HUMAN
  • B4DK47_HUMAN
  • Q5SZL3_HUMAN
  • Q5SZL4_HUMAN
  • Q5SZL5_HUMAN
  • Q5SZL6_HUMAN
  • Q5SZL8_HUMAN
  • Q5SZM1_HUMAN
  • Q5SZM2_HUMAN
  • U3KPS8_HUMAN
  • U3KPY5_HUMAN
  • U3KQ23_HUMAN
  • U3KQD8_HUMAN
  • U3KQQ0_HUMAN
genes like me logo Genes that share paralogs with TBC1D7: view

No data available for Paralogs for TBC1D7 Gene

Variants for TBC1D7 Gene

Sequence variations from dbSNP and Humsavar for TBC1D7 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs483352922 pathogenic, Macrocephaly 13,307,727(-) A/ coding_sequence_variant, frameshift, genic_downstream_transcript_variant
rs587777652 pathogenic, Macrocephaly 13,326,878(-) TCTCT/T coding_sequence_variant, frameshift
rs80189640 likely-benign, not specified 13,316,677(-) G/T coding_sequence_variant, genic_downstream_transcript_variant, intron_variant, missense_variant
rs9381921 likely-benign, not specified 13,316,684(-) C/T coding_sequence_variant, genic_downstream_transcript_variant, intron_variant, missense_variant
rs1000203086 -- 13,315,721(-) A/G genic_downstream_transcript_variant, intron_variant

Variation tolerance for TBC1D7 Gene

Residual Variation Intolerance Score: 67.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.51; 55.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBC1D7 Gene

Human Gene Mutation Database (HGMD)
TBC1D7
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBC1D7

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for TBC1D7 Gene

Disorders for TBC1D7 Gene

MalaCards: The human disease database

(5) MalaCards diseases for TBC1D7 Gene - From: HGMD, OMIM, ClinVar, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
macrocephaly/megalencephaly syndrome, autosomal recessive
  • mgcph
isolated megalencephaly
  • isolated macrencephaly
megalencephaly
  • macroencephaly
astigmatism
tuberous sclerosis
  • tuberous sclerosis 1
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TBCD7_HUMAN
  • Macrocephaly/megalencephaly syndrome, autosomal recessive (MGCPH) [MIM:248000]: A disorder characterized by abnormal enlargement of the cerebral hemispheres, mental retardation, large head, optic atrophy and underdeveloped skeletal musculature. Head enlargement may be evident at birth or the head may become abnormally large in the early years of life. Additional clinical features include behavioral abnormalities, psychosis, learning difficulties, prognathism, myopia and astigmatism. {ECO:0000269 PubMed:23687350, ECO:0000269 PubMed:24515783}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TBC1D7

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TBC1D7: view

No data available for Genatlas for TBC1D7 Gene

Publications for TBC1D7 Gene

  1. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PMID: 11042152) Zhang QH … Chen Z (Genome research 2000) 2 3 4 58
  2. Structural Basis of the Interaction between Tuberous Sclerosis Complex 1 (TSC1) and Tre2-Bub2-Cdc16 Domain Family Member 7 (TBC1D7). (PMID: 26893383) Qin J … Xu W (The Journal of biological chemistry 2016) 2 3 58
  3. TBC1D7 mutations are associated with intellectual disability, macrocrania, patellar dislocation, and celiac disease. (PMID: 24515783) Alfaiz AA … Reymond A (Human mutation 2014) 3 4 58
  4. Disruption of TBC1D7, a subunit of the TSC1-TSC2 protein complex, in intellectual disability and megalencephaly. (PMID: 23687350) Capo-Chichi JM … Michaud JL (Journal of medical genetics 2013) 3 4 58
  5. TBC1D7 is a third subunit of the TSC1-TSC2 complex upstream of mTORC1. (PMID: 22795129) Dibble CC … Manning BD (Molecular cell 2012) 3 4 58

Products for TBC1D7 Gene

Sources for TBC1D7 Gene

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