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    TBC1D2B TBC1 domain family member 2B [ Homo sapiens (human) ]

    Gene ID: 23102, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TBC1D2Bprovided by HGNC
    Official Full Name
    TBC1 domain family member 2Bprovided by HGNC
    Primary source
    HGNC:HGNC:29183
    See related
    Ensembl:ENSG00000167202 MIM:619152; AllianceGenome:HGNC:29183
    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
    NEDSGO
    Summary
    Predicted to enable GTPase activator activity. Involved in endocytosis. Located in cytosol and early endosome. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 23.9), gall bladder (RPKM 19.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TBC1D2B in Genome Data Viewer
    Location:
    15q24.3-q25.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (77994985..78077711, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (75857528..75940258, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (78287327..78370053, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 89 Neighboring gene COMM domain containing 4 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:78243991-78244491 Neighboring gene Sharpr-MPRA regulatory region 9982 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:78252702-78253247 Neighboring gene ADAMTS7 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6700 Neighboring gene uncharacterized LOC91450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9900 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9901 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6703 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:78376354-78376854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9909 Neighboring gene SH2 domain containing 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9910 Neighboring gene calcium and integrin binding family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6705

    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. Biallelic frameshift variant in the TBC1D2B gene in two siblings with progressive gingival overgrowth, fibrous dysplasia of face, and mental deterioration. Correia-Costa GR, et al. Clin Genet, 2022 Dec. PMID 36029130
    2. Biallelic loss-of-function variants in TBC1D2B cause a neurodevelopmental disorder with seizures and gingival overgrowth. Harms FL, et al. Hum Mutat, 2020 Sep. PMID 32623794
    3. ZEB1/NuRD complex suppresses TBC1D2b to stimulate E-cadherin internalization and promote metastasis in lung cancer. Manshouri R, et al. Nat Commun, 2019 Nov 12. PMID 31719531, Free PMC Article
    4. Rab GTPase-activating proteins in autophagy: regulation of endocytic and autophagy pathways by direct binding to human ATG8 modifiers. Popovic D, et al. Mol Cell Biol, 2012 May. PMID 22354992, Free PMC Article
    5. Functional dissection of Rab GTPases involved in primary cilium formation. Yoshimura S, et al. J Cell Biol, 2007 Jul 30. PMID 17646400, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Biallelic frameshift variant in the TBC1D2B gene in two siblings with progressive gingival overgrowth, fibrous dysplasia of face, and mental deterioration.
      Title: Biallelic frameshift variant in the TBC1D2B gene in two siblings with progressive gingival overgrowth, fibrous dysplasia of face, and mental deterioration.
    2. Biallelic loss-of-function variants in TBC1D2B cause a neurodevelopmental disorder with seizures and gingival overgrowth.
      Title: Biallelic loss-of-function variants in TBC1D2B cause a neurodevelopmental disorder with seizures and gingival overgrowth.
    3. TBC1D2b suppresses E-cadherin internalization, thus hindering cancer cell invasion and metastasis.
      Title: ZEB1/NuRD complex suppresses TBC1D2b to stimulate E-cadherin internalization and promote metastasis in lung cancer.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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
    Neurodevelopmental disorder with seizures and gingival overgrowth
    MedGen: C5543395 OMIM: 619323 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20166, KIAA1055

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    NOT involved_in regulation of cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    TBC1 domain family member 2B

    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_001387142.1 → NP_001374071.1  TBC1 domain family member 2B isoform c

      Status: VALIDATED

      Source sequence(s)
      AC090260, AC104758
      UniProtKB/TrEMBL
      B2RTQ2
      Conserved Domains (3) summary
      COG1196
      Location:338 → 552
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd01265
      Location:36 → 144
      PH_TBC1D2A; TBC1 domain family member 2A pleckstrin homology (PH) domain
      pfam00566
      Location:665 → 876
      RabGAP-TBC; Rab-GTPase-TBC domain

    2. NM_001387143.1 → NP_001374072.1  TBC1 domain family member 2B isoform d

      Status: VALIDATED

      Source sequence(s)
      AC090260, AC104758
      UniProtKB/TrEMBL
      B2RTQ2
      Conserved Domains (3) summary
      COG1196
      Location:337 → 551
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd01265
      Location:36 → 144
      PH_TBC1D2A; TBC1 domain family member 2A pleckstrin homology (PH) domain
      pfam00566
      Location:664 → 875
      RabGAP-TBC; Rab-GTPase-TBC domain

    3. NM_001387144.1 → NP_001374073.1  TBC1 domain family member 2B isoform e

      Status: VALIDATED

      Source sequence(s)
      AC090260, AC104758
      UniProtKB/TrEMBL
      B2RTQ2
      Conserved Domains (3) summary
      COG1196
      Location:338 → 552
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd01265
      Location:36 → 144
      PH_TBC1D2A; TBC1 domain family member 2A pleckstrin homology (PH) domain
      pfam00566
      Location:665 → 876
      RabGAP-TBC; Rab-GTPase-TBC domain

    4. NM_001387145.1 → NP_001374074.1  TBC1 domain family member 2B isoform f

      Status: VALIDATED

      Source sequence(s)
      AC090260, AC104758
      UniProtKB/TrEMBL
      B2RTQ2
      Conserved Domains (3) summary
      COG1196
      Location:226 → 440
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00566
      Location:553 → 764
      RabGAP-TBC; Rab-GTPase-TBC domain
      cl17171
      Location:9 → 32
      PH-like; Pleckstrin homology-like domain

    5. NM_001387146.1 → NP_001374075.1  TBC1 domain family member 2B isoform g

      Status: VALIDATED

      Source sequence(s)
      AC090260, AC104758
      UniProtKB/TrEMBL
      B2RTQ2
      Conserved Domains (3) summary
      COG1196
      Location:226 → 440
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00566
      Location:553 → 764
      RabGAP-TBC; Rab-GTPase-TBC domain
      cl17171
      Location:9 → 32
      PH-like; Pleckstrin homology-like domain

    6. NM_001387147.1 → NP_001374076.1  TBC1 domain family member 2B isoform h

      Status: VALIDATED

      Source sequence(s)
      AC090260, AC104758
      UniProtKB/TrEMBL
      B2RTQ2
      Conserved Domains (3) summary
      COG1196
      Location:226 → 440
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00566
      Location:553 → 764
      RabGAP-TBC; Rab-GTPase-TBC domain
      cl17171
      Location:9 → 32
      PH-like; Pleckstrin homology-like domain

    7. NM_001387148.1 → NP_001374077.1  TBC1 domain family member 2B isoform i

      Status: VALIDATED

      Source sequence(s)
      AC090260, AC104758
      UniProtKB/TrEMBL
      B2RTQ2
      Conserved Domains (3) summary
      COG1196
      Location:226 → 440
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00566
      Location:553 → 764
      RabGAP-TBC; Rab-GTPase-TBC domain
      cl17171
      Location:9 → 32
      PH-like; Pleckstrin homology-like domain

    8. NM_001387149.1 → NP_001374078.1  TBC1 domain family member 2B isoform j

      Status: VALIDATED

      Source sequence(s)
      AC090260, AC104758
      UniProtKB/TrEMBL
      B2RTQ2
      Conserved Domains (3) summary
      COG1196
      Location:227 → 402
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam00566
      Location:515 → 726
      RabGAP-TBC; Rab-GTPase-TBC domain
      cl17171
      Location:9 → 32
      PH-like; Pleckstrin homology-like domain

    9. NM_015079.6 → NP_055894.6  TBC1 domain family member 2B isoform b

      Status: VALIDATED

      Source sequence(s)
      AB028978, AC090260, AC104758, AL109773
      Consensus CDS
      CCDS32301.2
      UniProtKB/TrEMBL
      B2RTQ2
      Related
      ENSP00000387165.3, ENST00000409931.7
      Conserved Domains (3) summary
      COG1196
      Location:338 → 552
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd01265
      Location:36 → 144
      PH_TBC1D2A; TBC1 domain family member 2A pleckstrin homology (PH) domain
      pfam00566
      Location:665 → 876
      RabGAP-TBC; Rab-GTPase-TBC domain

    10. NM_144572.2 → NP_653173.1  TBC1 domain family member 2B isoform a

      See identical proteins and their annotated locations for NP_653173.1

      Status: VALIDATED

      Source sequence(s)
      AC090260, AC104758
      Consensus CDS
      CCDS45314.1
      UniProtKB/Swiss-Prot
      A7MD42, Q8N1F9, Q9NXM0, Q9UPU7
      UniProtKB/TrEMBL
      B2RTQ2
      Related
      ENSP00000300584.3, ENST00000300584.8
      Conserved Domains (3) summary
      COG1196
      Location:338 → 552
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd01265
      Location:36 → 144
      PH_TBC1D2A; TBC1 domain family member 2A pleckstrin homology (PH) domain
      pfam00566
      Location:665 → 876
      RabGAP-TBC; Rab-GTPase-TBC domain

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      77994985..78077711 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047432269.1 → XP_047288225.1  TBC1 domain family member 2B isoform X4

      UniProtKB/TrEMBL
      B2RTQ2

    2. XM_011521387.3 → XP_011519689.1  TBC1 domain family member 2B isoform X1

      UniProtKB/TrEMBL
      B2RTQ2
      Conserved Domains (4) summary
      cd01265
      Location:36 → 144
      PH_TBC1D2A; TBC1 domain family member 2A pleckstrin homology (PH) domain
      pfam00169
      Location:38 → 136
      PH; PH domain
      pfam00566
      Location:671 → 839
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam16515
      Location:339 → 376
      HIP1_clath_bdg; Clathrin-binding domain of Huntingtin-interacting protein 1

    3. XM_047432270.1 → XP_047288226.1  TBC1 domain family member 2B isoform X4

      UniProtKB/TrEMBL
      B2RTQ2

    4. XM_047432271.1 → XP_047288227.1  TBC1 domain family member 2B isoform X4

      UniProtKB/TrEMBL
      B2RTQ2

    5. XM_047432267.1 → XP_047288223.1  TBC1 domain family member 2B isoform X2

      UniProtKB/TrEMBL
      B2RTQ2

    6. XM_047432268.1 → XP_047288224.1  TBC1 domain family member 2B isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      75857528..75940258 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377555.1 → XP_054233530.1  TBC1 domain family member 2B isoform X4

      UniProtKB/TrEMBL
      B2RTQ2

    2. XM_054377552.1 → XP_054233527.1  TBC1 domain family member 2B isoform X1

      UniProtKB/TrEMBL
      B2RTQ2

    3. XM_054377556.1 → XP_054233531.1  TBC1 domain family member 2B isoform X4

      UniProtKB/TrEMBL
      B2RTQ2

    4. XM_054377557.1 → XP_054233532.1  TBC1 domain family member 2B isoform X4

      UniProtKB/TrEMBL
      B2RTQ2

    5. XM_054377553.1 → XP_054233528.1  TBC1 domain family member 2B isoform X2

      UniProtKB/TrEMBL
      B2RTQ2

    6. XM_054377554.1 → XP_054233529.1  TBC1 domain family member 2B isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UPU7.2 GenPept UniProtKB/Swiss-Prot:Q9UPU7

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