Aliases for DENND4B Gene

Aliases for DENND4B Gene

  • DENN Domain Containing 4B 2 3 5
  • KIAA0476 2 3 4
  • DENN Domain-Containing Protein 4B 3 4
  • DENN/MADD Domain Containing 4B 2 3
  • DENND4B 5

External Ids for DENND4B Gene

Previous HGNC Symbols for DENND4B Gene

  • KIAA0476

Previous GeneCards Identifiers for DENND4B Gene

  • GC01M150716
  • GC01M152168
  • GC01M125264

Summaries for DENND4B Gene

GeneCards Summary for DENND4B Gene

DENND4B (DENN Domain Containing 4B) is a Protein Coding gene. Diseases associated with DENND4B include Alkuraya-Kucinskas Syndrome and Boucher-Neuhauser Syndrome. Among its related pathways are RAB GEFs exchange GTP for GDP on RABs and Vesicle-mediated transport. Gene Ontology (GO) annotations related to this gene include Rab guanyl-nucleotide exchange factor activity. An important paralog of this gene is DENND4A.

UniProtKB/Swiss-Prot Summary for DENND4B Gene

  • Guanine nucleotide exchange factor (GEF) which may activate RAB10. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form.

Additional gene information for DENND4B Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for DENND4B Gene

Genomics for DENND4B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for DENND4B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DENND4B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for DENND4B

Top Transcription factor binding sites by QIAGEN in the DENND4B gene promoter:
  • ATF6
  • CREB
  • CUTL1
  • deltaCREB
  • ITF-2
  • N-Myc
  • Nkx2-5
  • Tal-1beta

Genomic Locations for DENND4B Gene

Genomic Locations for DENND4B Gene
chr1:153,929,501-153,946,718
(GRCh38/hg38)
Size:
17,218 bases
Orientation:
Minus strand
chr1:153,901,977-153,919,172
(GRCh37/hg19)
Size:
17,196 bases
Orientation:
Minus strand

Genomic View for DENND4B Gene

Genes around DENND4B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DENND4B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DENND4B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DENND4B Gene

Proteins for DENND4B Gene

  • Protein details for DENND4B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75064-DEN4B_HUMAN
    Recommended name:
    DENN domain-containing protein 4B
    Protein Accession:
    O75064
    Secondary Accessions:
    • Q5T4K0

    Protein attributes for DENND4B Gene

    Size:
    1496 amino acids
    Molecular mass:
    163847 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA32321.3; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=EAW53268.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

neXtProt entry for DENND4B Gene

Post-translational modifications for DENND4B Gene

  • Ubiquitination at Lys610
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for DENND4B Gene

Domains & Families for DENND4B Gene

Gene Families for DENND4B Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for DENND4B Gene

GenScript: Design optimal peptide antigens:
  • DENN domain-containing protein 4B (DEN4B_HUMAN)
genes like me logo Genes that share domains with DENND4B: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for DENND4B Gene

Function for DENND4B Gene

Molecular function for DENND4B Gene

UniProtKB/Swiss-Prot Function:
Guanine nucleotide exchange factor (GEF) which may activate RAB10. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form.

Phenotypes From GWAS Catalog for DENND4B Gene

Gene Ontology (GO) - Molecular Function for DENND4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity IEA --
GO:0005515 protein binding IEA --
GO:0017112 Rab guanyl-nucleotide exchange factor activity IDA 20937701
genes like me logo Genes that share ontologies with DENND4B: view
genes like me logo Genes that share phenotypes with DENND4B: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DENND4B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for DENND4B Gene

Localization for DENND4B Gene

Subcellular locations from UniProtKB/Swiss-Prot for DENND4B Gene

Golgi apparatus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DENND4B gene
Compartment Confidence
golgi apparatus 5
nucleus 4
cytosol 4
plasma membrane 3
extracellular 1
peroxisome 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (3)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DENND4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005794 Golgi apparatus IEA,IDA 20937701
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with DENND4B: view

Pathways & Interactions for DENND4B Gene

genes like me logo Genes that share pathways with DENND4B: view

Pathways by source for DENND4B Gene

Interacting Proteins for DENND4B Gene

Gene Ontology (GO) - Biological Process for DENND4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0032483 regulation of Rab protein signal transduction IDA 20937701
genes like me logo Genes that share ontologies with DENND4B: view

No data available for SIGNOR curated interactions for DENND4B Gene

Drugs & Compounds for DENND4B Gene

No Compound Related Data Available

Transcripts for DENND4B Gene

mRNA/cDNA for DENND4B Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DENND4B

Alternative Splicing Database (ASD) splice patterns (SP) for DENND4B Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16a · 16b ^
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14: - - -
SP15:
SP16:
SP17:
SP18:

ExUns: 17a · 17b · 17c ^ 18 ^ 19a · 19b ^ 20a · 20b ^ 21a · 21b ^ 22a · 22b · 22c · 22d ^ 23 ^ 24 ^ 25a · 25b ^ 26 ^ 27 ^ 28a · 28b · 28c · 28d
SP1: - -
SP2:
SP3:
SP4: - -
SP5: - -
SP6:
SP7:
SP8:
SP9:
SP10:
SP11: -
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:
SP18:

Relevant External Links for DENND4B Gene

GeneLoc Exon Structure for
DENND4B

Expression for DENND4B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for DENND4B Gene

Protein differential expression in normal tissues from HIPED for DENND4B Gene

This gene is overexpressed in Cervix (19.3), Peripheral blood mononuclear cells (14.2), CD8 Tcells (7.1), and Lymph node (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for DENND4B Gene



Protein tissue co-expression partners for DENND4B Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for DENND4B

SOURCE GeneReport for Unigene cluster for DENND4B Gene:

Hs.744878

Evidence on tissue expression from TISSUES for DENND4B Gene

  • Nervous system(4.5)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with DENND4B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for DENND4B Gene

Orthologs for DENND4B Gene

This gene was present in the common ancestor of animals.

Orthologs for DENND4B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia DENND4B 30 31
  • 99.69 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia DENND4B 30 31
  • 89.96 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia DENND4B 30 31
  • 89.06 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Dennd4b 30 17 31
  • 88.71 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Dennd4b 30
  • 88.61 (n)
Oppossum
(Monodelphis domestica)
Mammalia DENND4B 31
  • 88 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 31 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia DENND4B 31
  • 64 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii LOC798528 30
  • 61.12 (n)
DENND4B 31
  • 56 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Crag 31
  • 31 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea denn-4 31
  • 30 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.1014 31
  • 31 (a)
OneToMany
Species where no ortholog for DENND4B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for DENND4B Gene

ENSEMBL:
Gene Tree for DENND4B (if available)
TreeFam:
Gene Tree for DENND4B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DENND4B: view image

Paralogs for DENND4B Gene

Paralogs for DENND4B Gene

(2) SIMAP similar genes for DENND4B Gene using alignment to 3 proteins:

  • DEN4B_HUMAN
  • E9PAK5_HUMAN
  • H0YEF0_HUMAN
genes like me logo Genes that share paralogs with DENND4B: view

Variants for DENND4B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for DENND4B Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs1557853919 Likely Pathogenic: Short stature 153,939,040(-) G/A MISSENSE_VARIANT
rs201381125 Uncertain Significance: Short stature 153,934,248(-) C/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for DENND4B Gene

Variation tolerance for DENND4B Gene

Residual Variation Intolerance Score: 2.04% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.11; 87.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DENND4B Gene

Human Gene Mutation Database (HGMD)
DENND4B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
DENND4B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for DENND4B Gene

Disorders for DENND4B Gene

MalaCards: The human disease database

(4) MalaCards diseases for DENND4B Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with DENND4B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DENND4B Gene

Publications for DENND4B Gene

  1. Molecular cloning, structural analysis, and expression of a human IRLB, MYC promoter-binding protein: new DENN domain-containing protein family emerges. (PMID: 12906859) Semova N … Semov A (Genomics 2003) 2 3 4
  2. Characterization of cDNA clones in size-fractionated cDNA libraries from human brain. (PMID: 9455484) Seki N … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4
  3. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. (PMID: 20937701) Yoshimura S … Barr FA (The Journal of cell biology 2010) 3 4
  4. FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane. (PMID: 31056421) Ceccarelli DF … Sicheri F (Structure (London, England : 1993) 2019) 3
  5. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. (PMID: 29676528) Khanna R … Parnaik VK (The FEBS journal 2018) 3

Products for DENND4B Gene

Sources for DENND4B Gene