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TBC1D7 TBC1 domain family member 7 [ Homo sapiens (human) ]

Gene ID: 51256, updated on 17-Jun-2024

Summary

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Official Symbol
TBC1D7provided by HGNC
Official Full Name
TBC1 domain family member 7provided by HGNC
Primary source
HGNC:HGNC:21066
See related
Ensembl:ENSG00000145979 MIM:612655; AllianceGenome:HGNC:21066
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
TBC7; MGCPH; PIG51
Summary
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]
Expression
Ubiquitous expression in heart (RPKM 3.4), testis (RPKM 2.6) and 25 other tissues See more
Orthologs
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Genomic context

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See TBC1D7 in Genome Data Viewer
Location:
6p24.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (13304951..13328537, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (13178191..13201777, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (13305183..13328769, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene phosphatase and actin regulator 1 Neighboring gene TBC1D7-LOC100130357 readthrough Neighboring gene uncharacterized LOC105374933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16925 Neighboring gene Sharpr-MPRA regulatory region 805 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:13257894-13258394 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:13258395-13258895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24021 Neighboring gene uncharacterized LOC100130357 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:13273523-13274722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24023 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:13307473-13308672 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:13328608-13329114 Neighboring gene uncharacterized LOC124901261 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16927 Neighboring gene uncharacterized LOC105374936

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Discovery of TBC1D7 as a Potential Driver for Melanoma Cell Invasion. Qi TF, et al. Proteomics, 2020 Jul. PMID 32510182, Free PMC Article
  2. Activation of an oncogenic TBC1D7 (TBC1 domain family, member 7) protein in pulmonary carcinogenesis. Sato N, et al. Genes Chromosomes Cancer, 2010 Apr. PMID 20095038
  3. Structural Basis of the Interaction between Tuberous Sclerosis Complex 1 (TSC1) and Tre2-Bub2-Cdc16 Domain Family Member 7 (TBC1D7). Qin J, et al. J Biol Chem, 2016 Apr 15. PMID 26893383, Free PMC Article
  4. Disruption of TBC1D7, a subunit of the TSC1-TSC2 protein complex, in intellectual disability and megalencephaly. Capo-Chichi JM, et al. J Med Genet, 2013 Nov. PMID 23687350
  5. KIF2C: a novel link between Wnt/β-catenin and mTORC1 signaling in the pathogenesis of hepatocellular carcinoma. Wei S, et al. Protein Cell, 2021 Oct. PMID 32748349, Free PMC Article

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. KIF2C: a novel link between Wnt/beta-catenin and mTORC1 signaling in the pathogenesis of hepatocellular carcinoma.
    Title: KIF2C: a novel link between Wnt/β-catenin and mTORC1 signaling in the pathogenesis of hepatocellular carcinoma.
  2. Discovery of TBC1D7 as a Potential Driver for Melanoma Cell Invasion.
    Title: Discovery of TBC1D7 as a Potential Driver for Melanoma Cell Invasion.
  3. findings reveal that Akt activity determines the phosphorylation status of TBC1D7 at the phospho-switch Ser-124, which governs binding to either 14-3-3 or beta-TrCP2, resulting in increased or decreased stability of TBC1D7, respectively.
    Title: The tuberous sclerosis complex subunit TBC1D7 is stabilized by Akt phosphorylation-mediated 14-3-3 binding.
  4. Each TBC1D7 molecule interacts simultaneously with two parallel TSC1 helices from two TSC1 molecules, suggesting that TBC1D7 may stabilize the TSC complex by tethering the C-terminal ends of two TSC1 coiled-coils.
    Title: Structural Basis of the Interaction between Tuberous Sclerosis Complex 1 (TSC1) and Tre2-Bub2-Cdc16 Domain Family Member 7 (TBC1D7).
  5. DNA mutational studies allow enlarging the phenotypic spectrum associated with TBC1D7 mutations and defining a TBC1D7 syndrome.
    Title: TBC1D7 mutations are associated with intellectual disability, macrocrania, patellar dislocation, and celiac disease.
  6. Study suggests that disruption of TBC1D7 causes ID but without the other typical features found in TSC.
    Title: Disruption of TBC1D7, a subunit of the TSC1-TSC2 protein complex, in intellectual disability and megalencephaly.
  7. TBC1D7 knockdown results in increased mTORC1 signaling.
    Title: TBC1D7 is a third subunit of the TSC1-TSC2 complex upstream of mTORC1.
  8. Immunohistochemistry of NSCLC tumor tissue suggested an association of TBC1D7 expression with poor prognosis for NSCLC patients; Treatment of lung cancer cells using siRNA against TBC1D7, suppressed its expression and inhibited cell growth.
    Title: Activation of an oncogenic TBC1D7 (TBC1 domain family, member 7) protein in pulmonary carcinogenesis.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Macrocephaly/megalencephaly syndrome, autosomal recessive
MedGen: C3806412 OMIM: 248000 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies new susceptibility loci for migraine.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ32666, dJ257A7.3, DKFZp686N2317

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GTPase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables small GTPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in activation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in activation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cellular response to starvation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of TOR signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of TOR signaling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of TOR signaling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of TORC1 signaling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to growth factor IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of TSC1-TSC2 complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of TSC1-TSC2 complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in ciliary basal body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in lysosomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
TBC1 domain family member 7
Names
TBC domain family 7
TS complex subunit 3
Tre2-Bub2-Cdc16 Domain Family Member 7
cell migration-inducing protein 23

NCBI Reference Sequences (RefSeq)

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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_033862.1 RefSeqGene

    Range
    5047..28633
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001143964.4 → NP_001137436.1  TBC1 domain family member 7 isoform a

    See identical proteins and their annotated locations for NP_001137436.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 6 encode the same isoform (a).
    Source sequence(s)
    AB449888, AK223445, BC050465, DB079098
    UniProtKB/Swiss-Prot
    E7EV96, Q2TU37, Q53F44, Q5SZL7, Q86VM8, Q96MB8, Q9P0N9
    UniProtKB/TrEMBL
    Q5SZL4
    Related
    ENSP00000394425.1, ENST00000422136.5
    Conserved Domains (1) summary
    cl02495
    Location:147 → 251
    RabGAP-TBC; Rab-GTPase-TBC domain

  2. NM_001143965.4 → NP_001137437.1  TBC1 domain family member 7 isoform a

    See identical proteins and their annotated locations for NP_001137437.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 6 encode the same isoform (a).
    Source sequence(s)
    BC007054, BC050465, DB079098
    UniProtKB/Swiss-Prot
    E7EV96, Q2TU37, Q53F44, Q5SZL7, Q86VM8, Q96MB8, Q9P0N9
    UniProtKB/TrEMBL
    Q5SZL4
    Related
    ENSP00000348813.4, ENST00000356436.8
    Conserved Domains (1) summary
    cl02495
    Location:147 → 251
    RabGAP-TBC; Rab-GTPase-TBC domain

  3. NM_001143966.4 → NP_001137438.1  TBC1 domain family member 7 isoform b

    See identical proteins and their annotated locations for NP_001137438.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 5' UTR and lacks an in-frame exon in the 5' coding region compared to variant 1, which results in a shorter isoform (b) than isoform a.
    Source sequence(s)
    BC050465, DB079098
    Consensus CDS
    CCDS47376.1
    UniProtKB/TrEMBL
    Q5SZL6
    Related
    ENSP00000368609.2, ENST00000379307.6
    Conserved Domains (1) summary
    cl02495
    Location:120 → 220
    RabGAP-TBC; Rab-GTPase-TBC domain

  4. NM_001258457.3 → NP_001245386.1  TBC1 domain family member 7 isoform c

    See identical proteins and their annotated locations for NP_001245386.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in the 5' UTR and lacks an in-frame exon in the central coding region compared to variant 1, which results in a shorter isoform (c) than isoform a.
    Source sequence(s)
    AY542308, BC050465, DB079098
    Consensus CDS
    CCDS58995.1
    UniProtKB/TrEMBL
    Q5SZL4
    Related
    ENSP00000343100.4, ENST00000343141.8
    Conserved Domains (1) summary
    cl02495
    Location:129 → 201
    RabGAP-TBC; Rab-GTPase-TBC domain

  5. NM_001318805.2 → NP_001305734.1  TBC1 domain family member 7 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 6 encode the same isoform (a).
    Source sequence(s)
    BC050465, BX354770, DB079098
    UniProtKB/Swiss-Prot
    E7EV96, Q2TU37, Q53F44, Q5SZL7, Q86VM8, Q96MB8, Q9P0N9
    UniProtKB/TrEMBL
    Q5SZL4
    Conserved Domains (1) summary
    cl02495
    Location:147 → 251
    RabGAP-TBC; Rab-GTPase-TBC domain

  6. NM_001318806.2 → NP_001305735.1  TBC1 domain family member 7 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks multiple 3' coding exons its transcription extends past a splice site used in variant 1, resulting in a different 3' coding region and 3' UTR. The encoded isoform (d) has a shorter, distinct C-terminus compared to isoform a.
    Source sequence(s)
    AL589984, AL833474
    Consensus CDS
    CCDS83062.1
    UniProtKB/TrEMBL
    U3KPY5
    Related
    ENSP00000475355.1, ENST00000606370.5

  7. NM_016495.6 → NP_057579.1  TBC1 domain family member 7 isoform a

    See identical proteins and their annotated locations for NP_057579.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1, 2, 3, and 6 encode the same isoform (a).
    Source sequence(s)
    AF151073, BC050465, DB079098
    UniProtKB/Swiss-Prot
    E7EV96, Q2TU37, Q53F44, Q5SZL7, Q86VM8, Q96MB8, Q9P0N9
    UniProtKB/TrEMBL
    Q5SZL4
    Related
    ENSP00000368602.3, ENST00000379300.8
    Conserved Domains (1) summary
    cl02495
    Location:147 → 251
    RabGAP-TBC; Rab-GTPase-TBC domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    13304951..13328537 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    13178191..13201777 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P0N9.1 GenPept UniProtKB/Swiss-Prot:Q9P0N9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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