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

Gene ID: 23329, updated on 5-Mar-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, Apr 2022]
Expression
Broad expression in brain (RPKM 3.2), salivary gland (RPKM 1.1) and 21 other tissues See more
Orthologs
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Genomic context

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Location:
12q14.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (64759484..64881033)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (64738311..64860047)
105.20220307 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)

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

  • 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 small GTPase 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 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_2023_10

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

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