TBC1D3 Gene (Protein Coding)

TBC1 Domain Family Member 3

GC17M038181
GIFtS:
29
See more...

Aliases for TBC1D3 Gene

Aliases for TBC1D3 Gene

  • TBC1 Domain Family Member 3 2 3 4 5
  • TBC1D3A 2 3 4
  • PRC17 2 3 4
  • Rab GTPase-Activating Protein PRC17 3 4
  • Prostate Cancer Gene 17 Protein 3 4
  • Protein TRE17-Alpha 3 4
  • TBC1 Domain Family, Member 3F 3
  • TBC1 Domain Family, Member 3 2
  • TBC1 Domain Family Member 3C 3
  • TBC1 Domain Family Member 3L 3
  • Prostate Cancer Gene 17 2
  • DKFZp434P2235 2
  • TBC1D3C 3
  • TBC1D3D 3
  • TBC1D3F 3
  • TBC1D3L 3
  • TBC1D3 5

External Ids for TBC1D3 Gene

Previous GeneCards Identifiers for TBC1D3 Gene

  • GC17P036015
  • GC17M036712
  • GC17P033358
  • GC17M033413
  • GC17M033592
  • GC17M033594
  • GC17M036338

Summaries for TBC1D3 Gene

GeneCards Summary for TBC1D3 Gene

TBC1D3 (TBC1 Domain Family Member 3) is a Protein Coding gene. Diseases associated with TBC1D3 include Prostate Cancer. Among its related pathways are Vesicle-mediated transport and TBC/RABGAPs. Gene Ontology (GO) annotations related to this gene include GTPase activator activity. An important paralog of this gene is TBC1D3C.

UniProtKB/Swiss-Prot Summary for TBC1D3 Gene

  • Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11.

Additional gene information for TBC1D3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TBC1D3 Gene

Genomics for TBC1D3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for TBC1D3 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH17J038255 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 9 -63.7 -63746 3.8 ZSCAN16 NR2C1 NONO ZIC2 CEBPB VEZF1 SAP130 KLF7 ZNF341 KLF9 NPEPPSP1 TBC1D3 MRPL45 piR-49732-241
GH17J038297 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 9.1 -104.5 -104546 2.2 TBP ZBTB10 SP1 FEZF1 MNT IKZF1 SMAD5 HES1 ZFP64 ZNF217 MRPL45 LOC105371760 lnc-GPR179-4 TBC1D3 NONHSAG021648.2 GPR179
GH17J038276 Enhancer 1.1 Ensembl ENCODE dbSUPER 9.3 -84.6 -84564 1.8 FEZF1 IKZF1 KLF7 ZEB2 ZNF843 SP2 PRDM6 TCF7L2 PRDM10 SP7 TBC1D3 RF00017-2363 L13714-201 MRPL45 LOC105371760
GH17J039174 Promoter/Enhancer 1.2 Ensembl ENCODE dbSUPER 6.3 -982.3 -982339 1.6 CTCF ZNF513 REST VEZF1 TRIM22 SMC3 RAD21 MYRF ZBTB48 ZNF48 CACNB1 RPL19 PSMB3 TBC1D3 ARL5C ENSG00000266101 lnc-ARL5C-2 LOC105371768
GH17J038323 Enhancer 0.9 FANTOM5 Ensembl ENCODE 7.3 -133.4 -133354 4.2 GABPA ZEB2 RBM22 SPI1 CEBPG ATF4 ZNF148 GATA2 PAF1 RFX1 SOCS7 MRPL45 TBC1D3 lnc-GPR179-1 piR-45035-087 GPR179
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TBC1D3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TBC1D3

Top Transcription factor binding sites by QIAGEN in the TBC1D3 gene promoter:
  • c-Rel
  • GATA-3
  • Hlf
  • STAT1
  • STAT1alpha
  • STAT1beta
  • STAT2
  • STAT3
  • STAT4
  • STAT5A

Genomic Locations for TBC1D3 Gene

Latest Assembly
chr17:38,181,659-38,192,555
(GRCh38/hg38)
Size:
10,897 bases
Orientation:
Minus strand

Previous Assembly
chr17:36,337,528-36,348,621
(GRCh37/hg19 by Entrez Gene)
Size:
11,094 bases
Orientation:
Minus strand

Genomic View for TBC1D3 Gene

Genes around TBC1D3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBC1D3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBC1D3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TBC1D3 Gene

Proteins for TBC1D3 Gene

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  • Protein details for TBC1D3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IZP1-TBC3A_HUMAN
    Recommended name:
    TBC1 domain family member 3
    Protein Accession:
    Q8IZP1
    Secondary Accessions:
    • A6NGX2
    • A8K007
    • Q6DCB4
    • Q9H0B9
    • Q9UDD4

    Protein attributes for TBC1D3 Gene

    Size:
    549 amino acids
    Molecular mass:
    62187 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • TBC1D3 is encoded by a collection of very similar paralogs with multiple copies of each paralog, some human genomes encoding well over 50 copies depending on ethnic origin of the donor.

    Alternative splice isoforms for TBC1D3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBC1D3 Gene

Protein Expression for TBC1D3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TBC1D3 Gene

  • Ubiquitinated by a CUL7-based E3 ligase, which leads to proteasomal degradation.
  • Palmitoylation is required for membrane localization and protects TBC1D3 from ubiquitination.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TBC1D3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for TBC1D3 Gene

Domains & Families for TBC1D3 Gene

Gene Families for TBC1D3 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for TBC1D3 Gene

InterPro:
Blocks:
  • RabGAP/TBC domain
ProtoNet:

Suggested Antigen Peptide Sequences for TBC1D3 Gene

GenScript: Design optimal peptide antigens:
  • TBC1 domain family, member 3 (B9A6J9_HUMAN)
  • TBC1D3 protein (Q6DCB4_HUMAN)
  • Rab GTPase-activating protein PRC17 (TBC3A_HUMAN)
genes like me logo Genes that share domains with TBC1D3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for TBC1D3 Gene

Function for TBC1D3 Gene

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  6. Cell Lines for research

Molecular function for TBC1D3 Gene

UniProtKB/Swiss-Prot Function:
Acts as a GTPase activating protein for RAB5. Does not act on RAB4 or RAB11.

Phenotypes From GWAS Catalog for TBC1D3 Gene

Gene Ontology (GO) - Molecular Function for TBC1D3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IBA 21873635
GO:0031267 small GTPase binding IBA --
genes like me logo Genes that share ontologies with TBC1D3: view

Animal Models for research

miRNA for TBC1D3 Gene

miRTarBase miRNAs that target TBC1D3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBC1D3

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TBC1D3 Gene

Localization for TBC1D3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBC1D3 Gene

Cell membrane. Lipid-anchor. Note=Associated with lipid rafts.

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TBC1D3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0031901 early endosome membrane TAS --
genes like me logo Genes that share ontologies with TBC1D3: view

No data available for Subcellular locations from COMPARTMENTS for TBC1D3 Gene

Pathways & Interactions for TBC1D3 Gene

PathCards logo

SuperPathways for TBC1D3 Gene

genes like me logo Genes that share pathways with TBC1D3: view

Pathways by source for TBC1D3 Gene

3 Reactome pathways for TBC1D3 Gene

Gene Ontology (GO) - Biological Process for TBC1D3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IBA 21873635
GO:0090630 activation of GTPase activity IBA 21873635
GO:1902017 NOT regulation of cilium assembly IMP 17646400
genes like me logo Genes that share ontologies with TBC1D3: view

No data available for SIGNOR curated interactions for TBC1D3 Gene

Drugs & Compounds for TBC1D3 Gene

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No Compound Related Data Available

Transcripts for TBC1D3 Gene

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mRNA/cDNA for TBC1D3 Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TBC1D3

Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D3 Gene

No ASD Table

Relevant External Links for TBC1D3 Gene

GeneLoc Exon Structure for
TBC1D3

Expression for TBC1D3 Gene

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  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TBC1D3 Gene

mRNA expression in normal human tissues for TBC1D3 Gene
mRNA expression by GTEx for TBC1D3 GenemRNA expression by BioGPS for TBC1D3 Gene

Protein differential expression in normal tissues from HIPED for TBC1D3 Gene

This gene is overexpressed in Adipocyte (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for TBC1D3 Gene



Protein tissue co-expression partners for TBC1D3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TBC1D3

SOURCE GeneReport for Unigene cluster for TBC1D3 Gene:

Hs.735975

mRNA Expression by UniProt/SwissProt for TBC1D3 Gene:

Q8IZP1-TBC3A_HUMAN
Tissue specificity: Expressed in liver, skeletal muscle, kidney, pancreas, spleen, testis, ovary, small intestine and peripheral blood leukocytes. Overexpressed in prostate cancers.
genes like me logo Genes that share expression patterns with TBC1D3: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for TBC1D3 Gene

Orthologs for TBC1D3 Gene

Evolution for TBC1D3 Gene

ENSEMBL:
Gene Tree for TBC1D3 (if available)
TreeFam:
Gene Tree for TBC1D3 (if available)

No data available for Orthologs for TBC1D3 Gene

Paralogs for TBC1D3 Gene

Paralogs for TBC1D3 Gene

(16) SIMAP similar genes for TBC1D3 Gene using alignment to 7 proteins:

  • TBC3A_HUMAN
  • A6NDL0_HUMAN
  • B9A6J9_HUMAN
  • E5RGJ9_HUMAN
  • F6U074_HUMAN
  • H0YB77_HUMAN
  • Q6DCB4_HUMAN
genes like me logo Genes that share paralogs with TBC1D3: view

Variants for TBC1D3 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TBC1D3 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs1567681955 - p.Gln526Pro

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TBC1D3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TBC1D3 Gene

Variant ID Type Subtype PubMed ID
dgv1463n106 CNV duplication 24896259
dgv1754e59 CNV duplication 20981092
dgv1755e59 CNV duplication 20981092
dgv911e212 CNV gain 25503493
dgv912e212 CNV loss 25503493
dgv913e212 CNV loss 25503493
dgv914e212 CNV gain 25503493
dgv915e212 CNV gain 25503493
dgv916e212 CNV loss 25503493
esv2758688 CNV gain+loss 17122850
esv28567 CNV gain+loss 19812545
esv3334247 CNV duplication 20981092
esv3383710 CNV duplication 20981092
esv3572853 CNV gain 25503493
esv3573020 CNV gain 25503493
esv3582628 CNV loss 25503493
esv3582629 CNV loss 25503493
nsv1070402 CNV deletion 25765185
nsv1078413 CNV duplication 25765185
nsv1078415 CNV duplication 25765185
nsv1128762 CNV duplication 24896259
nsv1141305 CNV duplication 24896259
nsv1153123 CNV duplication 26484159
nsv428341 CNV gain+loss 18775914
nsv471398 CNV gain 19718026
nsv471507 CNV gain 19718026
nsv820624 CNV duplication 20802225
nsv833432 CNV gain+loss 17160897
nsv833435 CNV gain+loss 17160897
nsv953890 CNV duplication 24416366
nsv953891 CNV duplication 24416366
nsv960598 CNV duplication 23825009

Variation tolerance for TBC1D3 Gene

Gene Damage Index Score: 0.01; 0.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TBC1D3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBC1D3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBC1D3 Gene

Disorders for TBC1D3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TBC1D3 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
prostate cancer
  • prostate cancer, somatic
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TBC1D3

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with TBC1D3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TBC1D3 Gene

Publications for TBC1D3 Gene

  1. The Tre2 (USP6) oncogene is a hominoid-specific gene. (PMID: 12604796) Paulding CA … Haber DA (Proceedings of the National Academy of Sciences of the United States of America 2003) 2 3 4
  2. PRC17, a novel oncogene encoding a Rab GTPase-activating protein, is amplified in prostate cancer. (PMID: 12359748) Pei L … Li J (Cancer research 2002) 2 3 4
  3. Ubiquitination and degradation of the hominoid-specific oncoprotein TBC1D3 is regulated by protein palmitoylation. (PMID: 23578663) Kong C … Stahl PD (Biochemical and biophysical research communications 2013) 3 4
  4. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PMID: 16625196) Zody MC … Nusbaum C (Nature 2006) 3 4
  5. TBC1D3, a hominoid oncoprotein, is encoded by a cluster of paralogues located on chromosome 17q12. (PMID: 16863688) Hodzic D … Stahl PD (Genomics 2006) 2 3

ExternalLinks

View latest publications for TBC1D3 gene in Mastermind

Products for TBC1D3 Gene

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Sources for TBC1D3 Gene