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    TBC1D21 TBC1 domain family member 21 [ Homo sapiens (human) ]

    Gene ID: 161514, updated on 27-Nov-2024

    Summary

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    Official Symbol
    TBC1D21provided by HGNC
    Official Full Name
    TBC1 domain family member 21provided by HGNC
    Primary source
    HGNC:HGNC:28536
    See related
    Ensembl:ENSG00000167139 MIM:620387; AllianceGenome:HGNC:28536
    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
    MgcRabGAP
    Summary
    Enables GTPase activator activity and small GTPase binding activity. Predicted to be involved in sperm axoneme assembly and sperm mitochondrial sheath assembly. Located in extracellular exosome. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward testis (RPKM 8.2) See more
    Orthologs
    mouse all
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    Genomic context

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    See TBC1D21 in Genome Data Viewer
    Location:
    15q24.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (73873564..73910024)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (71690893..71727352)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74165905..74181555)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74149333-74150025 Neighboring gene uncharacterized LOC102723657 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74173695-74174256 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:74179454-74179712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74194653-74195154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74214297-74215284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74215285-74216270 Neighboring gene LOXL1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74219309-74220142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74220143-74220976 Neighboring gene Sharpr-MPRA regulatory region 13651 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74229856-74230455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74232882-74233777 Neighboring gene lysyl oxidase like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74244872-74245555 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:74249081-74250280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9731 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9732 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:74280304-74281503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9737 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6644 Neighboring gene stomatin like 1

    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. RAB10 Interacts with the Male Germ Cell-Specific GTPase-Activating Protein during Mammalian Spermiogenesis. Lin YH, et al. Int J Mol Sci, 2017 Jan 5. PMID 28067790, Free PMC Article
    2. Novel common variants and susceptible haplotype for exfoliation glaucoma specific to Asian population. Nakano M, et al. Sci Rep, 2014 Jun 18. PMID 24938310, Free PMC Article
    3. Deficiency of the Tbc1d21 gene causes male infertility with morphological abnormalities of the sperm mitochondria and flagellum in mice. Wang YY, et al. PLoS Genet, 2020 Sep. PMID 32976492, Free PMC Article
    4. Identification and characterization of a novel Rab GTPase-activating protein in spermatids. Lin YH, et al. Int J Androl, 2011 Oct. PMID 21128978
    5. 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

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Deficiency of the Tbc1d21 gene causes male infertility with morphological abnormalities of the sperm mitochondria and flagellum in mice.
      Title: Deficiency of the Tbc1d21 gene causes male infertility with morphological abnormalities of the sperm mitochondria and flagellum in mice.
    2. Data indicate that single-nucleotide polymorphisms (SNPs) distributing in not only lysyl oxidase-like 1 gene (LOXL1) but also TBC1 domain family member 21 protein (TBC1D21) and promyelocytic leukemia protein (PML).
      Title: Novel common variants and susceptible haplotype for exfoliation glaucoma specific to Asian population.
    3. MgcRabGAP is involved in acrosome/acroplaxome formation and cytoskeletal reorganization via Rab activity during mammalian spermiogenesis
      Title: Identification and characterization of a novel Rab GTPase-activating protein in spermatids.
    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

    EBI GWAS Catalog

    Description
    Novel common variants and susceptible haplotype for exfoliation glaucoma specific to Asian population.
    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

    • MGC34741

    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 actin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in flagellated sperm motility ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in plasma membrane to endosome transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    NOT involved_in regulation of cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in sperm axoneme assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in sperm mitochondrial sheath assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in spermatogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in acrosomal vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasmic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular exosome HDA PubMed 
    located_in sperm midpiece ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    TBC1 domain family member 21
    Names
    male germ cell Rab GTPase-activating protein
    male germ cell-specific expressed, containing a RabGAP domain

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001286434.2 → NP_001273363.1  TBC1 domain family member 21 isoform 2

      See identical proteins and their annotated locations for NP_001273363.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AB449907, AC018943, BC033516, HY018107
      Consensus CDS
      CCDS66822.1
      UniProtKB/TrEMBL
      H3BTA9
      Related
      ENSP00000439325.2, ENST00000535547.6
      Conserved Domains (1) summary
      smart00164
      Location:26 → 251
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    2. NM_153356.3 → NP_699187.1  TBC1 domain family member 21 isoform 1

      See identical proteins and their annotated locations for NP_699187.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB449907, AC018943, BC033516, HY018107
      Consensus CDS
      CCDS10252.1
      UniProtKB/Swiss-Prot
      B9A6M2, Q8IYX1
      UniProtKB/TrEMBL
      H3BTA9
      Related
      ENSP00000300504.2, ENST00000300504.7
      Conserved Domains (1) summary
      smart00164
      Location:62 → 287
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    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
      73873564..73910024
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521281.4 → XP_011519583.1  TBC1 domain family member 21 isoform X3

      UniProtKB/TrEMBL
      H3BTA9
      Conserved Domains (1) summary
      smart00164
      Location:62 → 287
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    2. XM_047432198.1 → XP_047288154.1  TBC1 domain family member 21 isoform X6

    3. XM_011521283.3 → XP_011519585.1  TBC1 domain family member 21 isoform X5

      UniProtKB/TrEMBL
      H3BTA9
      Conserved Domains (1) summary
      smart00164
      Location:62 → 287
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    4. XM_011521282.3 → XP_011519584.1  TBC1 domain family member 21 isoform X4

      UniProtKB/TrEMBL
      H3BTA9
      Conserved Domains (1) summary
      smart00164
      Location:62 → 287
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    5. XM_006720410.5 → XP_006720473.1  TBC1 domain family member 21 isoform X2

      Conserved Domains (1) summary
      smart00164
      Location:26 → 251
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    6. XM_006720409.5 → XP_006720472.1  TBC1 domain family member 21 isoform X1

      Conserved Domains (1) summary
      smart00164
      Location:62 → 287
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    7. XM_006720411.4 → XP_006720474.1  TBC1 domain family member 21 isoform X8

      Conserved Domains (1) summary
      smart00164
      Location:23 → 188
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    8. XM_011521284.4 → XP_011519586.1  TBC1 domain family member 21 isoform X7

      Conserved Domains (1) summary
      smart00164
      Location:34 → 199
      TBC; Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      71690893..71727352
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377375.1 → XP_054233350.1  TBC1 domain family member 21 isoform X3

    2. XM_054377378.1 → XP_054233353.1  TBC1 domain family member 21 isoform X6

    3. XM_054377377.1 → XP_054233352.1  TBC1 domain family member 21 isoform X5

    4. XM_054377376.1 → XP_054233351.1  TBC1 domain family member 21 isoform X4

    5. XM_054377374.1 → XP_054233349.1  TBC1 domain family member 21 isoform X2

    6. XM_054377373.1 → XP_054233348.1  TBC1 domain family member 21 isoform X1

    7. XM_054377380.1 → XP_054233355.1  TBC1 domain family member 21 isoform X8

    8. XM_054377379.1 → XP_054233354.1  TBC1 domain family member 21 isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IYX1.1 GenPept UniProtKB/Swiss-Prot:Q8IYX1

    Gene LinkOut

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

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