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    TBC1D30 TBC1 domain family member 30 [ Homo sapiens (human) ]

    Gene ID: 23329, updated on 27-Nov-2024

    Summary

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    Official Symbol
    TBC1D30provided by HGNC
    Official Full Name
    TBC1 domain family member 30provided by HGNC
    Primary source
    HGNC:HGNC:29164
    See related
    Ensembl:ENSG00000111490 MIM:615077; AllianceGenome:HGNC:29164
    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
    Summary
    Enables GTPase activator activity and small GTPase binding activity. Involved in negative regulation of cilium assembly and positive regulation of GTPase activity. Located in ciliary basal body; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in brain (RPKM 3.2), salivary gland (RPKM 1.1) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TBC1D30 in Genome Data Viewer
    Location:
    12q14.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (64759484..64881033)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (64738311..64860047)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (65153264..65274813)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Ras association domain family member 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:65019275-65019991 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:65035223-65035726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:65041527-65042250 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:65046125-65046302 Neighboring gene microRNA 548c Neighboring gene microRNA 548z Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6599 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6600 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:65066263-65066452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:65068096-65068875 Neighboring gene Sharpr-MPRA regulatory region 4654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:65151732-65152612 Neighboring gene small nucleolar RNA U13 Neighboring gene glucosamine (N-acetyl)-6-sulfatase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4628 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:65219125-65219632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6601 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:65252401-65252902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:65252903-65253402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6603 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:65282633-65283275 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:65283276-65283917 Neighboring gene ribosomal protein L7 pseudogene 39 Neighboring gene long intergenic non-protein coding RNA 2389 Neighboring gene uncharacterized LOC124903125 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:65325441-65325942 Neighboring gene long intergenic non-protein coding RNA 2231 Neighboring gene RNA, U6atac small nuclear 42, pseudogene

    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. Cargo-selective apical exocytosis in epithelial cells is conducted by Myo5B, Slp4a, Vamp7, and Syntaxin 3. Vogel GF, et al. J Cell Biol, 2015 Nov 9. PMID 26553929, Free PMC Article
    2. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. Ishibashi K, et al. Genes Cells, 2009 Jan. PMID 19077034
    3. Common genetic variation and performance on standardized cognitive tests. Cirulli ET, et al. Eur J Hum Genet, 2010 Jul. PMID 20125193, Free PMC Article
    4. GAPs galore! A survey of putative Ras superfamily GTPase activating proteins in man and Drosophila. Bernards A. Biochim Biophys Acta, 2003 Mar 17. PMID 12618308
    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 (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    EBI GWAS Catalog

    Description
    Common genetic variation and performance on standardized cognitive tests.
    EBI GWAS 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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0984

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol 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 30

    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_001330186.2 → NP_001317115.1  TBC1 domain family member 30 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter but has the same N- and C-termini as isoform 1.
      Source sequence(s)
      AB449914, AC025262, AC078815, BM678817, DC377016
      UniProtKB/Swiss-Prot
      Q9Y2I9

    2. NM_001330187.2 → NP_001317116.1  TBC1 domain family member 30 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains alternate exons in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1. Both variants 3 and 4 encode the same isoform (3).
      Source sequence(s)
      AB449914, AC025262, AC078815, BM310544, BM678817, HY146277
      Consensus CDS
      CCDS81708.1
      UniProtKB/TrEMBL
      F8VZ81
      Related
      ENSP00000501371.1, ENST00000674237.1
      Conserved Domains (2) summary
      pfam00566
      Location:19 → 199
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam15733
      Location:360 → 488
      DUF4682; Domain of unknown function (DUF4682)

    3. NM_001330188.2 → NP_001317117.1  TBC1 domain family member 30 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains alternate exons in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus than isoform 1. Both variants 3 and 4 encode the same isoform (3).
      Source sequence(s)
      AB449914, AC025262, AC078815, BM310544, BM678817
      Consensus CDS
      CCDS81708.1
      UniProtKB/TrEMBL
      F8VZ81
      Conserved Domains (2) summary
      pfam00566
      Location:19 → 199
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam15733
      Location:360 → 488
      DUF4682; Domain of unknown function (DUF4682)

    4. NM_001364838.2 → NP_001351767.1  TBC1 domain family member 30 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC025262, AC078815
      Consensus CDS
      CCDS81708.1
      UniProtKB/TrEMBL
      F8VZ81
      Conserved Domains (2) summary
      pfam00566
      Location:19 → 199
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam15733
      Location:360 → 488
      DUF4682; Domain of unknown function (DUF4682)

    5. NM_015279.2 → NP_056094.1  TBC1 domain family member 30 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB449914, AC025262, AC078815, BM678817, DC377016
      Consensus CDS
      CCDS53813.1
      UniProtKB/Swiss-Prot
      Q9Y2I9
      Related
      ENSP00000440207.1, ENST00000539867.6
      Conserved Domains (2) summary
      pfam00566
      Location:133 → 313
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam15733
      Location:474 → 603
      DUF4682; Domain of unknown function (DUF4682)

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      64759484..64881033
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428595.1 → XP_047284551.1  TBC1 domain family member 30 isoform X1

    2. XM_047428596.1 → XP_047284552.1  TBC1 domain family member 30 isoform X2

      UniProtKB/Swiss-Prot
      B3KP01, B9A6M9, E7EMW4, F5GYJ9, Q9Y2I9
      Related
      ENSP00000440640.2, ENST00000542120.6

    3. XM_024448903.2 → XP_024304671.1  TBC1 domain family member 30 isoform X3

      Conserved Domains (2) summary
      pfam00566
      Location:296 → 476
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam15733
      Location:637 → 741
      DUF4682; Domain of unknown function (DUF4682)

    4. XM_024448904.2 → XP_024304672.1  TBC1 domain family member 30 isoform X5

      Conserved Domains (2) summary
      pfam00566
      Location:19 → 199
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam15733
      Location:360 → 508
      DUF4682; Domain of unknown function (DUF4682)

    5. XM_047428599.1 → XP_047284555.1  TBC1 domain family member 30 isoform X6

      UniProtKB/TrEMBL
      F8VZ81

    6. XM_047428600.1 → XP_047284556.1  TBC1 domain family member 30 isoform X7

    7. XM_011538078.3 → XP_011536380.1  TBC1 domain family member 30 isoform X4

      Conserved Domains (2) summary
      pfam00566
      Location:133 → 313
      RabGAP-TBC; Rab-GTPase-TBC domain
      pfam15733
      Location:474 → 623
      DUF4682; Domain of unknown function (DUF4682)

    8. XM_047428597.1 → XP_047284553.1  TBC1 domain family member 30 isoform X5

    9. XM_047428601.1 → XP_047284557.1  TBC1 domain family member 30 isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      64738311..64860047
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054371560.1 → XP_054227535.1  TBC1 domain family member 30 isoform X1

    2. XM_054371561.1 → XP_054227536.1  TBC1 domain family member 30 isoform X2

      UniProtKB/Swiss-Prot
      B3KP01, B9A6M9, E7EMW4, F5GYJ9, Q9Y2I9

    3. XM_054371562.1 → XP_054227537.1  TBC1 domain family member 30 isoform X3

    4. XM_054371565.1 → XP_054227540.1  TBC1 domain family member 30 isoform X5

    5. XM_054371566.1 → XP_054227541.1  TBC1 domain family member 30 isoform X6

      UniProtKB/TrEMBL
      F8VZ81

    6. XM_054371567.1 → XP_054227542.1  TBC1 domain family member 30 isoform X7

    7. XM_054371563.1 → XP_054227538.1  TBC1 domain family member 30 isoform X4

    8. XM_054371564.1 → XP_054227539.1  TBC1 domain family member 30 isoform X5

    9. XM_054371568.1 → XP_054227543.1  TBC1 domain family member 30 isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y2I9.2 GenPept UniProtKB/Swiss-Prot:Q9Y2I9

    Gene LinkOut

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

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