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TBC1D1 TBC1 domain family member 1 [ Homo sapiens (human) ]

Gene ID: 23216, updated on 20-Mar-2020

Summary

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Official Symbol
TBC1D1provided by HGNC
Official Full Name
TBC1 domain family member 1provided by HGNC
Primary source
HGNC:HGNC:11578
See related
Ensembl:ENSG00000065882 MIM:609850
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TBC; TBC1
Summary
TBC1D1 is the founding member of a family of proteins sharing a 180- to 200-amino acid TBC domain presumed to have a role in regulating cell growth and differentiation. These proteins share significant homology with TRE2 (USP6; MIM 604334), yeast Bub2, and CDC16 (MIM 603461) (White et al., 2000 [PubMed 10965142]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in endometrium (RPKM 22.4), kidney (RPKM 18.2) and 24 other tissues See more
Orthologs
mouse all

Genomic context

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See TBC1D1 in Genome Data Viewer
Location:
4p14
Exon count:
31
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (37891084..38139175)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (37889606..38140796)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene phosphoglucomutase 2 Neighboring gene heterogeneous nuclear ribonucleoprotein R pseudogene 3 Neighboring gene uncharacterized LOC105374407 Neighboring gene pituitary tumor-transforming 2 Neighboring gene proteasome activator subunit 2 pseudogene 4 Neighboring gene mitochondrial ribosomal protein S33 pseudogene 2 Neighboring gene skeletal muscle cis-regulatory module in TBC1D1 intron Neighboring gene uncharacterized LOC105374408 Neighboring gene uncharacterized LOC105374409

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. Structural and population-based evaluations of TBC1D1 p.Arg125Trp. Richardson TG, et al. PLoS One, 2013. PMID 23667688, Free PMC Article
  2. Exploratory study on association of genetic variation in TBC1D1 with antipsychotic-induced weight gain. Brandl EJ, et al. Hum Psychopharmacol, 2013 Mar. PMID 23364847
  3. Exercise alleviates lipid-induced insulin resistance in human skeletal muscle-signaling interaction at the level of TBC1 domain family member 4. Pehmøller C, et al. Diabetes, 2012 Nov. PMID 22851577, Free PMC Article
  4. Exercise increases TBC1D1 phosphorylation in human skeletal muscle. Jessen N, et al. Am J Physiol Endocrinol Metab, 2011 Jul. PMID 21505148, Free PMC Article
  5. R125W coding variant in TBC1D1 confers risk for familial obesity and contributes to linkage on chromosome 4p14 in the French population. Meyre D, et al. Hum Mol Genet, 2008 Jun 15. PMID 18325908

See all (49) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TBC1D1-Ser(231) phosphorylation and/or 14-3-3 binding partially mediates AMPK-governed glucose homeostasis and muscle glucose uptake in a context-dependent manner.
    Title: A Tbc1d1 <sup>Ser231Ala</sup>-knockin mutation partially impairs AICAR- but not exercise-induced muscle glucose uptake in mice.
  2. data demonstrate heterozygous deactivating TBC1D1 mutations in CAKUT patients with a similar renal and ureteral phenotype, and provide evidence that TBC1D1 mutations may contribute to CAKUT
    Title: Whole-exome sequencing identifies mutations of TBC1D1 encoding a Rab-GTPase-activating protein in patients with congenital anomalies of the kidneys and urinary tract (CAKUT).
  3. AS160 and TBC1D1 phosphorylations were evident 30 min after exercise.
    Title: Sustained AS160 and TBC1D1 phosphorylations in human skeletal muscle 30 min after a single bout of exercise.
  4. Data show that TBC1D1 is expressed and phosphorylated in response to glucose in these cells.
    Title: Expression, phosphorylation and function of the Rab-GTPase activating protein TBC1D1 in pancreatic beta-cells.
  5. Moderate association of rs9852 indicates an influence of TBC1D1 for antipsychotic-induced weight gain.
    Title: Exploratory study on association of genetic variation in TBC1D1 with antipsychotic-induced weight gain.
  6. R125W mutation occurs in a location of the TBC1D1 PTB domain that is predicted to have a function in a putative protein:protein interaction.
    Title: Structural and population-based evaluations of TBC1D1 p.Arg125Trp.
  7. Data suggest that insulin increases phosphorylation of signaling nexus TBC1D1 independent of prior exercise or lipid/Intralipid administration.
    Title: Exercise alleviates lipid-induced insulin resistance in human skeletal muscle-signaling interaction at the level of TBC1 domain family member 4.
  8. TBC1D1 is Ser237 phosphorylated and binding capacity to 14-3-3 protein is increased in skeletal muscle following exercise.
    Title: Exercise-induced TBC1D1 Ser237 phosphorylation and 14-3-3 protein binding capacity in human skeletal muscle.
  9. [review] The question of a mechanism for increased phosphorylation of Ser237-TBC1D1 after exercise has, so far, not had a straightforward experimental approach for a direct answer in humans undergoing in vivo exercise.
    Title: Of mice and men: filling gaps in the TBC1D1 story.
  10. A single bout of exercise regulates TBC1D1 and AS160 phosphorylation on multiple sites in human skeletal muscle.
    Title: Exercise increases TBC1D1 phosphorylation in human skeletal muscle.
Submit: New GeneRIF Correction See all GeneRIFs (17)

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

NHGRI GWAS Catalog

Description
A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population.
NHGRI GWA Catalog
Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations.
NHGRI GWA Catalog
Genome-wide association study of periodontal pathogen colonization.
NHGRI GWA 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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1108

Gene Ontology Provided by GOA

Function Evidence Code Pubs
GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
Rab GTPase binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
activation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
membrane organization TAS
Traceable Author Statement
more info
  
NOT regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
regulation of protein localization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
  
nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
TBC1 domain family member 1
Names
TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1

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.

mRNA and Protein(s)

  1. NM_001253912.2 → NP_001240841.1  TBC1 domain family member 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has multiple differences in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK074954, AK295746, AW364769, BC050321, BQ672157, CR996632, DB036208
    Consensus CDS
    CCDS58897.1
    UniProtKB/Swiss-Prot
    Q86TI0
    UniProtKB/TrEMBL
    Q8NC59
    Related
    ENSP00000423651.1, ENST00000508802.5
    Conserved Domains (5) summary
    smart00164
    Location:891 → 1028
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 371
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:543 → 838
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:789 → 839
    DUF3350; Domain of unknown function (DUF3350)

  2. NM_001253913.1 → NP_001240842.1  TBC1 domain family member 1 isoform 3

    See identical proteins and their annotated locations for NP_001240842.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a large portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which has a significantly shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC098680, AC108933, AK057182, AK074954, AW364769
    UniProtKB/TrEMBL
    Q8NC59
    Conserved Domains (1) summary
    smart00164
    Location:2 → 111
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  3. NM_001253914.1 → NP_001240843.1  TBC1 domain family member 1 isoform 3

    See identical proteins and their annotated locations for NP_001240843.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a large portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which has a significantly shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK074954, CR996632
    UniProtKB/TrEMBL
    Q8NC59
    Related
    ENST00000407365.5
    Conserved Domains (1) summary
    smart00164
    Location:2 → 111
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  4. NM_001253915.1 → NP_001240844.1  TBC1 domain family member 1 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a large portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (4) has a significantly shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK074954, BC032337, CR996632
    UniProtKB/TrEMBL
    Q8NC59

  5. NM_015173.4 → NP_055988.2  TBC1 domain family member 1 isoform 1

    See identical proteins and their annotated locations for NP_055988.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB449881, AK074954, BC014529, BC050321, DB036208
    Consensus CDS
    CCDS33972.1
    UniProtKB/Swiss-Prot
    Q86TI0
    UniProtKB/TrEMBL
    B9A6J6, Q6PJJ8, Q8NC59
    Related
    ENSP00000261439.4, ENST00000261439.9
    Conserved Domains (4) summary
    smart00164
    Location:797 → 1014
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 371
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:695 → 745
    DUF3350; Domain of unknown function (DUF3350)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    37891084..38139175
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513659.2 → XP_011511961.1  TBC1 domain family member 1 isoform X1

    Conserved Domains (5) summary
    smart00164
    Location:924 → 1141
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:563 → 871
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:822 → 872
    DUF3350; Domain of unknown function (DUF3350)

  2. XM_011513660.3 → XP_011511962.1  TBC1 domain family member 1 isoform X2

    Conserved Domains (5) summary
    smart00164
    Location:911 → 1128
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:563 → 858
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:809 → 859
    DUF3350; Domain of unknown function (DUF3350)

  3. XM_011513662.3 → XP_011511964.1  TBC1 domain family member 1 isoform X5

    Conserved Domains (4) summary
    smart00164
    Location:884 → 1101
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:782 → 832
    DUF3350; Domain of unknown function (DUF3350)

  4. XM_011513663.3 → XP_011511965.1  TBC1 domain family member 1 isoform X6

    Conserved Domains (4) summary
    smart00164
    Location:871 → 1088
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:769 → 819
    DUF3350; Domain of unknown function (DUF3350)

  5. XM_011513664.3 → XP_011511966.1  TBC1 domain family member 1 isoform X7

    Conserved Domains (4) summary
    smart00164
    Location:870 → 1087
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:768 → 818
    DUF3350; Domain of unknown function (DUF3350)

  6. XM_017007918.2 → XP_016863407.1  TBC1 domain family member 1 isoform X8

  7. XM_011513665.3 → XP_011511967.1  TBC1 domain family member 1 isoform X10

    Conserved Domains (4) summary
    smart00164
    Location:830 → 1047
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:728 → 778
    DUF3350; Domain of unknown function (DUF3350)

  8. XM_011513666.3 → XP_011511968.1  TBC1 domain family member 1 isoform X11

    Conserved Domains (4) summary
    smart00164
    Location:817 → 1034
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam11830
    Location:715 → 765
    DUF3350; Domain of unknown function (DUF3350)

  9. XM_005262646.3 → XP_005262703.1  TBC1 domain family member 1 isoform X3

    See identical proteins and their annotated locations for XP_005262703.1

    Conserved Domains (5) summary
    smart00164
    Location:904 → 1121
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 371
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:543 → 851
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:802 → 852
    DUF3350; Domain of unknown function (DUF3350)

  10. XM_005262647.3 → XP_005262704.1  TBC1 domain family member 1 isoform X4

    See identical proteins and their annotated locations for XP_005262704.1

    Conserved Domains (5) summary
    smart00164
    Location:891 → 1108
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 371
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:543 → 838
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:789 → 839
    DUF3350; Domain of unknown function (DUF3350)

  11. XM_017007919.2 → XP_016863408.1  TBC1 domain family member 1 isoform X9

  12. XM_017007920.2 → XP_016863409.1  TBC1 domain family member 1 isoform X12

  13. XM_017007922.1 → XP_016863411.1  TBC1 domain family member 1 isoform X15

  14. XM_011513668.2 → XP_011511970.1  TBC1 domain family member 1 isoform X16

    Conserved Domains (3) summary
    cd00934
    Location:21 → 150
    PTB; Phosphotyrosine-binding (PTB) PH-like fold
    cd01269
    Location:164 → 391
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:563 → 788
    CytochromB561_N; Cytochrome B561, N terminal

  15. XM_005262649.3 → XP_005262706.1  TBC1 domain family member 1 isoform X13

    Conserved Domains (4) summary
    smart00164
    Location:775 → 992
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd01269
    Location:35 → 242
    PTB_TBC1D1_like; TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain
    pfam09786
    Location:414 → 722
    CytochromB561_N; Cytochrome B561, N terminal
    pfam11830
    Location:673 → 723
    DUF3350; Domain of unknown function (DUF3350)

  16. XM_017007921.2 → XP_016863410.1  TBC1 domain family member 1 isoform X14

  17. XM_006714001.3 → XP_006714064.1  TBC1 domain family member 1 isoform X17

    Conserved Domains (2) summary
    smart00164
    Location:175 → 392
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam11830
    Location:73 → 123
    DUF3350; Domain of unknown function (DUF3350)

  18. XM_011513670.3 → XP_011511972.1  TBC1 domain family member 1 isoform X18

    Related
    ENSP00000478039.1, ENST00000615497.4
    Conserved Domains (2) summary
    smart00164
    Location:123 → 340
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    pfam11830
    Location:21 → 71
    DUF3350; Domain of unknown function (DUF3350)

RNA

  1. XR_001741181.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86TI0.2 GenPept UniProtKB/Swiss-Prot:Q86TI0

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