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

Gene ID: 23102, updated on 3-Nov-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, Nov 2024]
Expression
Ubiquitous expression in ovary (RPKM 23.9), gall bladder (RPKM 19.7) and 25 other tissues See more
Orthologs
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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 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 (31) 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)

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

  • 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
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in early endosome IDA
Inferred from Direct Assay
more info
 PubMed 

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

  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

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

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

  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

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

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

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

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

  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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