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TBC1D2 TBC1 domain family member 2 [ Homo sapiens (human) ]

Gene ID: 55357, updated on 3-Apr-2024

Summary

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Official Symbol
TBC1D2provided by HGNC
Official Full Name
TBC1 domain family member 2provided by HGNC
Primary source
HGNC:HGNC:18026
See related
Ensembl:ENSG00000095383 MIM:609871; AllianceGenome:HGNC:18026
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
PARIS1; PARIS-1; TBC1D2A
Summary
Enables GTPase activator activity and cadherin binding activity. Involved in positive regulation of GTPase activity. Located in several cellular components, including cytoplasmic vesicle; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in lung (RPKM 7.7), urinary bladder (RPKM 3.8) and 23 other tissues See more
Orthologs
mouse all
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Genomic context

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See TBC1D2 in Genome Data Viewer
Location:
9q22.33
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (98198998..98255649, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (110370941..110427596, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (100961280..101017931, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100833954-100834454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100836915-100837721 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100849215-100849889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100849890-100850563 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:100852934-100853493 Neighboring gene tripartite motif containing 14 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28691 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20115 Neighboring gene N-acetylneuraminate synthase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28692 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:100921913-100922413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100924760-100925260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28693 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100933363-100934198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100935871-100936704 Neighboring gene Sharpr-MPRA regulatory region 7304 Neighboring gene coronin 2A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100953772-100954426 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20117 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100957663-100958179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100960535-100961402 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100961403-100962270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100963511-100964012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100964013-100964512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100965136-100965636 Neighboring gene Sharpr-MPRA regulatory region 378 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:100984952-100986151 Neighboring gene ADP ribosylation factor like GTPase 8B pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101010111-101011028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101011029-101011945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28695 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28696 Neighboring gene MPRA-validated peak7303 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:101036136-101036669 Neighboring gene NANOG hESC enhancer GRCh37_chr9:101036702-101037236 Neighboring gene NANOG hESC enhancer GRCh37_chr9:101037237-101037769 Neighboring gene microRNA 6854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101042021-101042706 Neighboring gene Sharpr-MPRA regulatory region 5055 Neighboring gene GATA motif-containing MPRA enhancer 175 Neighboring gene gamma-aminobutyric acid type B receptor subunit 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101122073-101122573 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:101134501-101135189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28697 Neighboring gene Sharpr-MPRA regulatory region 1904 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:101151090-101151268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101158435-101159110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101159111-101159786 Neighboring gene NANOG hESC enhancer GRCh37_chr9:101164028-101164529 Neighboring gene MPRA-validated peak7304 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:101257622-101258821 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101270847-101271377 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_103859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:101328229-101328729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28698 Neighboring gene Sharpr-MPRA regulatory region 14650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:101372736-101373728 Neighboring gene septin 7 pseudogene 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:101430118-101430303 Neighboring gene uncharacterized LOC124902228

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. Serological cloning of PARIS-1: a new TBC domain-containing, immunogenic tumor antigen from a prostate cancer cell line. Zhou Y, et al. Biochem Biophys Res Commun, 2002 Jan 18. PMID 11785977
  2. The TBC/RabGAP Armus coordinates Rac1 and Rab7 functions during autophagy. Carroll B, et al. Dev Cell, 2013 Apr 15. PMID 23562278, Free PMC Article
  3. miR-17-5p regulates endocytic trafficking through targeting TBC1D2/Armus. Serva A, et al. PLoS One, 2012. PMID 23285084, Free PMC Article
  4. Armus is a Rac1 effector that inactivates Rab7 and regulates E-cadherin degradation. Frasa MA, et al. Curr Biol, 2010 Feb 9. PMID 20116244
  5. Replication of top markers of a genome-wide association study in multiple sclerosis in Spain. Cavanillas ML, et al. Genes Immun, 2011 Mar. PMID 20944657

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. integration of Rac1 and Rab7 activities by Armus provides an important regulatory node for E-cadherin turnover and stability of cell-cell contacts
    Title: Armus is a Rac1 effector that inactivates Rab7 and regulates E-cadherin degradation.
  2. Armus expression induces autophagosome accumulation in keratinocytes.
    Title: The TBC/RabGAP Armus coordinates Rac1 and Rab7 functions during autophagy.
  3. TBC1D2/Armus, a GAP of Rab7 GTPase, is reported as a novel target of miR-17.
    Title: miR-17-5p regulates endocytic trafficking through targeting TBC1D2/Armus.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Replication of top markers of a genome-wide association study in multiple sclerosis in Spain.
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

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

  • FLJ10702, FLJ16244, FLJ42782, DKFZp761D1823

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 cadherin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein 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 positive regulation of GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
NOT involved_in regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in anchoring junction IEA
Inferred from Electronic Annotation
more info
  
located_in cell junction 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
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
TBC1 domain family member 2A
Names
TBC1 domain family, member 2A
armus
prostate antigen recognized and identified by SEREX 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_001267571.2 → NP_001254500.1  TBC1 domain family member 2A isoform 1

    See identical proteins and their annotated locations for NP_001254500.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB449882, AY026527, BX091503, DB167423
    Consensus CDS
    CCDS75865.1
    UniProtKB/Swiss-Prot
    B3KWD1, B4DQ05, B9A6J7, Q59EU0, Q5TBQ5, Q6IPC7, Q7L1K8, Q8WYT1, Q9BYX2, Q9H6A2, Q9NSH4
    Related
    ENSP00000481721.1, ENST00000465784.7
    Conserved Domains (3) summary
    smart00164
    Location:625 → 837
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd01265
    Location:47 → 147
    PH_TBC1D2A; TBC1 domain family member 2A pleckstrin homology (PH) domain
    pfam00169
    Location:47 → 139
    PH; PH domain

  2. NM_001267572.1 → NP_001254501.1  TBC1 domain family member 2A isoform 3

    See identical proteins and their annotated locations for NP_001254501.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and represents the use of an alternate promoter, compared to variant 1, which results in the use of an in-frame downstream start codon and a protein (isoform 3) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AY026527, BC028918, BX091503
    Consensus CDS
    CCDS59137.1
    Related
    ENSP00000364203.1, ENST00000375063.5
    Conserved Domains (1) summary
    smart00164
    Location:165 → 377
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  3. NM_001410988.1 → NP_001397917.1  TBC1 domain family member 2A isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL137073, AL360081, AL591502
    Consensus CDS
    CCDS94445.1
    Related
    ENSP00000364205.1, ENST00000375064.5

  4. NM_018421.4 → NP_060891.3  TBC1 domain family member 2A isoform 2

    See identical proteins and their annotated locations for NP_060891.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame segment in the 3' coding region, compared to variant 1, which results in a protein (isoform 2) with a shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AL137073, AL591502, AY026527, BX091503
    Consensus CDS
    CCDS35080.1
    UniProtKB/Swiss-Prot
    Q9BYX2
    Related
    ENSP00000364207.5, ENST00000375066.6
    Conserved Domains (3) summary
    smart00164
    Location:625 → 817
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs
    cd01265
    Location:47 → 147
    PH_TBC1D2A; TBC1 domain family member 2A pleckstrin homology (PH) domain
    pfam00169
    Location:47 → 139
    PH; PH domain

RNA

  1. NR_051978.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon in the 5' coding region, compared to variant 1, which results in a frameshift and early stop codon. The transcript is sufficiently abundant to represent as a RefSeq; however, the predicted protein is not represented because the product is significantly truncated and the transcript is a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB449882, AK124772, AY026527, BX091503
    Related
    ENST00000342112.9

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    98198998..98255649 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518843.3 → XP_011517145.1  TBC1 domain family member 2A isoform X2

    See identical proteins and their annotated locations for XP_011517145.1

    Conserved Domains (1) summary
    smart00164
    Location:165 → 377
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  2. XM_024447606.2 → XP_024303374.1  TBC1 domain family member 2A isoform X2

    Conserved Domains (1) summary
    smart00164
    Location:165 → 377
    TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

  3. XM_047423565.1 → XP_047279521.1  TBC1 domain family member 2A isoform X1

  4. XM_011518844.4 → XP_011517146.1  TBC1 domain family member 2A isoform X3

    Conserved Domains (2) summary
    cd01265
    Location:47 → 147
    PH_TBC1D2A; TBC1 domain family member 2A pleckstrin homology (PH) domain
    pfam00169
    Location:47 → 139
    PH; PH domain

RNA

  1. XR_929824.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    110370941..110427596 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054363233.1 → XP_054219208.1  TBC1 domain family member 2A isoform X2

  2. XM_054363234.1 → XP_054219209.1  TBC1 domain family member 2A isoform X2

  3. XM_054363232.1 → XP_054219207.1  TBC1 domain family member 2A isoform X1

  4. XM_054363235.1 → XP_054219210.1  TBC1 domain family member 2A isoform X3

RNA

  1. XR_008488045.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BYX2.3 GenPept UniProtKB/Swiss-Prot:Q9BYX2

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