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

    Gene ID: 55357, updated on 10-Dec-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, Dec 2024]
    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_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (98198998..98255649, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (110370941..110427596, complement)
    RS_2024_09 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 (28) 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)

    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 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 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    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_2024_08

    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

      UniProtKB/TrEMBL
      B3KY99

    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

      UniProtKB/TrEMBL
      B3KY99

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

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