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Aliases for DENND1B Gene

Aliases for DENND1B Gene

  • DENN Domain Containing 1B 2 3 5
  • Connecdenn 2 2 3 4
  • Family With Sequence Similarity 31, Member B 2 3
  • DENN/MADD Domain Containing 1B 2 3
  • C1orf218 3 4
  • FAM31B 3 4
  • Chromosome 1 Open Reading Frame 218 2
  • DENN Domain-Containing Protein 1B 3
  • Protein FAM31B 4
  • C1ORF18 3

External Ids for DENND1B Gene

Previous HGNC Symbols for DENND1B Gene

  • FAM31B
  • C1orf218

Previous GeneCards Identifiers for DENND1B Gene

  • GC01M194253
  • GC01M195746
  • GC01M195788
  • GC01M168677

Summaries for DENND1B Gene

Entrez Gene Summary for DENND1B Gene

  • Clathrin (see MIM 118955)-mediated endocytosis is a major mechanism for internalization of proteins and lipids. Members of the connecdenn family, such as DENND1B, function as guanine nucleotide exchange factors (GEFs) for the early endosomal small GTPase RAB35 (MIM 604199) and bind to clathrin and clathrin adaptor protein-2 (AP2; see MIM 601024). Thus, connecdenns link RAB35 activation with the clathrin machinery (Marat and McPherson, 2010 [PubMed 20154091]).[supplied by OMIM, Nov 2010]

GeneCards Summary for DENND1B Gene

DENND1B (DENN Domain Containing 1B) is a Protein Coding gene. Diseases associated with DENND1B include Asthma and Interleukin-7 Receptor Alpha Deficiency. Among its related pathways are RAB GEFs exchange GTP for GDP on RABs and Vesicle-mediated transport. GO annotations related to this gene include Rab guanyl-nucleotide exchange factor activity. An important paralog of this gene is DENND1A.

UniProtKB/Swiss-Prot for DENND1B Gene

  • Guanine nucleotide exchange factor (GEF) for RAB35 that acts as a regulator of T-cell receptor (TCR) internalization in TH2 cells (PubMed:20154091, PubMed:20937701, PubMed:24520163, PubMed:26774822). Acts by promoting the exchange of GDP to GTP, converting inactive GDP-bound RAB35 into its active GTP-bound form (PubMed:20154091, PubMed:20937701). Plays a role in clathrin-mediated endocytosis (PubMed:20154091). Controls cytokine production in TH2 lymphocytes by controlling the rate of TCR internalization and routing to endosomes: acts by mediating clathrin-mediated endocytosis of TCR via its interaction with the adapter protein complex 2 (AP-2) and GEF activity (PubMed:26774822). Dysregulation leads to impaired TCR down-modulation and recycling, affecting cytokine production in TH2 cells (PubMed:26774822).

Additional gene information for DENND1B Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DENND1B Gene

Genomics for DENND1B Gene

Regulatory Elements for DENND1B Gene

Enhancers for DENND1B Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H197675 1.1 Ensembl ENCODE 11 +106.4 106375 0 BRD4 MXI1 IRF2 MAX ZNF384 CEBPG ZBTB40 YY1 IRF9 POLR2A DENND1B GC01P197674 GC01M197685 ENSG00000207139
GH01H197736 0.8 Ensembl ENCODE 11.6 +45.3 45314 1 ZNF217 SMARCE1 CTBP1 GATA3 CEBPB DPF2 EP300 ENSG00000224901 DENND1B C1orf53 LHX9 GC01P197735 FAM204BP
GH01H197838 0.8 Ensembl ENCODE 11 -56.7 -56726 1 FOSL1 GATA3 JUN FOS BATF DENND1B C1orf53
GH01H197733 0.7 ENCODE 11.6 +48.6 48570 0 SOX5 SOX13 GATAD2A HMG20A PPARG RARA PRDM6 CEBPA TCF7 BCL6 ENSG00000224901 DENND1B C1orf53 LHX9 RPL24P5 EEF1A1P32
GH01H198154 1.8 FANTOM5 ENCODE dbSUPER 2.5 -375.7 -375708 6 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZBTB41 NEK7 DENND1B PTPRC C1orf53 GC01M198198
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around DENND1B on UCSC Golden Path with GeneCards custom track

Genomic Location for DENND1B Gene

Chromosome:
1
Start:
197,504,748 bp from pter
End:
197,782,175 bp from pter
Size:
277,428 bases
Orientation:
Minus strand

Genomic View for DENND1B Gene

Genes around DENND1B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DENND1B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DENND1B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DENND1B Gene

Proteins for DENND1B Gene

  • Protein details for DENND1B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6P3S1-DEN1B_HUMAN
    Recommended name:
    DENN domain-containing protein 1B
    Protein Accession:
    Q6P3S1
    Secondary Accessions:
    • B5MD89
    • D3PFD5
    • Q5T3B8
    • Q5T3B9
    • Q5T3C1
    • Q5TAI8
    • Q6B0I8
    • Q8NDT1
    • Q8TBE6
    • Q9H774
    • Q9NXU2

    Protein attributes for DENND1B Gene

    Size:
    775 amino acids
    Molecular mass:
    86552 Da
    Quaternary structure:
    • Interacts with RAB35 (PubMed:24520163, PubMed:22065758). Interacts with clathrin heavy chain/CLTC (PubMed:20154091). Interacts with components of the adapter protein complex 2 (AP-2) AP2A2 and AP2B1 (PubMed:20154091). Interacts with CD3E (By similarity).
    SequenceCaution:
    • Sequence=AAH74735.2; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA90918.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB15024.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=EAW91280.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for DENND1B Gene

    Alternative splice isoforms for DENND1B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DENND1B Gene

Post-translational modifications for DENND1B Gene

  • Phosphorylated on serine and/or threonine, possibly regulating the guanine nucleotide exchange factor (GEF) activity.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for DENND1B Gene

Domains & Families for DENND1B Gene

Gene Families for DENND1B Gene

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

Protein Domains for DENND1B Gene

Graphical View of Domain Structure for InterPro Entry

Q6P3S1

UniProtKB/Swiss-Prot:

DEN1B_HUMAN :
  • The FXDXF motif mediates interaction the AP-2 complex.
Domain:
  • The FXDXF motif mediates interaction the AP-2 complex.
  • The clathrin box motif mediates interaction with clathrin.
genes like me logo Genes that share domains with DENND1B: view

Function for DENND1B Gene

Molecular function for DENND1B Gene

UniProtKB/Swiss-Prot Function:
Guanine nucleotide exchange factor (GEF) for RAB35 that acts as a regulator of T-cell receptor (TCR) internalization in TH2 cells (PubMed:20154091, PubMed:20937701, PubMed:24520163, PubMed:26774822). Acts by promoting the exchange of GDP to GTP, converting inactive GDP-bound RAB35 into its active GTP-bound form (PubMed:20154091, PubMed:20937701). Plays a role in clathrin-mediated endocytosis (PubMed:20154091). Controls cytokine production in TH2 lymphocytes by controlling the rate of TCR internalization and routing to endosomes: acts by mediating clathrin-mediated endocytosis of TCR via its interaction with the adapter protein complex 2 (AP-2) and GEF activity (PubMed:26774822). Dysregulation leads to impaired TCR down-modulation and recycling, affecting cytokine production in TH2 cells (PubMed:26774822).

Phenotypes From GWAS Catalog for DENND1B Gene

Gene Ontology (GO) - Molecular Function for DENND1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0017112 Rab guanyl-nucleotide exchange factor activity TAS --
GO:0017137 Rab GTPase binding IEA --
genes like me logo Genes that share ontologies with DENND1B: view
genes like me logo Genes that share phenotypes with DENND1B: view

Animal Models for DENND1B Gene

MGI Knock Outs for DENND1B:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for DENND1B
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for DENND1B Gene

Localization for DENND1B Gene

Subcellular locations from UniProtKB/Swiss-Prot for DENND1B Gene

Cytoplasm, cytosol. Cytoplasmic vesicle, clathrin-coated vesicle.

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 DENND1B gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 2
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DENND1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0016607 nuclear speck IDA --
GO:0030136 clathrin-coated vesicle IEA --
GO:0031410 cytoplasmic vesicle IEA --
genes like me logo Genes that share ontologies with DENND1B: view

Pathways & Interactions for DENND1B Gene

genes like me logo Genes that share pathways with DENND1B: view

Pathways by source for DENND1B Gene

Gene Ontology (GO) - Biological Process for DENND1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0015031 protein transport IEA --
GO:0032456 endocytic recycling ISS --
GO:0035745 T-helper 2 cell cytokine production IMP 26774822
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with DENND1B: view

No data available for SIGNOR curated interactions for DENND1B Gene

Drugs & Compounds for DENND1B Gene

No Compound Related Data Available

Transcripts for DENND1B Gene

Unigene Clusters for DENND1B Gene

DENN/MADD domain containing 1B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for DENND1B
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for DENND1B Gene

No ASD Table

Relevant External Links for DENND1B Gene

GeneLoc Exon Structure for
DENND1B
ECgene alternative splicing isoforms for
DENND1B

Expression for DENND1B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DENND1B Gene

Protein differential expression in normal tissues from HIPED for DENND1B Gene

This gene is overexpressed in Pancreatic juice (49.0) and Islet of Langerhans (20.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for DENND1B Gene



Protein tissue co-expression partners for DENND1B Gene

NURSA nuclear receptor signaling pathways regulating expression of DENND1B Gene:

DENND1B

SOURCE GeneReport for Unigene cluster for DENND1B Gene:

Hs.125056

mRNA Expression by UniProt/SwissProt for DENND1B Gene:

Q6P3S1-DEN1B_HUMAN
Tissue specificity: Highly expressed in dendritic and natural killer cells and at lower levels in other myeloid lineage cells and in pituitary. Significantly up-regulated in effector memory T-cells as compared with naive T-cells.

Evidence on tissue expression from TISSUES for DENND1B Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with DENND1B: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for DENND1B Gene

Orthologs for DENND1B Gene

This gene was present in the common ancestor of animals.

Orthologs for DENND1B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DENND1B 33 34
  • 99.78 (n)
dog
(Canis familiaris)
Mammalia DENND1B 33 34
  • 91.17 (n)
mouse
(Mus musculus)
Mammalia Dennd1b 33 16 34
  • 85.72 (n)
rat
(Rattus norvegicus)
Mammalia Dennd1b 33
  • 85.02 (n)
cow
(Bos Taurus)
Mammalia DENND1B 33 34
  • 80.8 (n)
oppossum
(Monodelphis domestica)
Mammalia DENND1B 34
  • 48 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DENND1B 34
  • 39 (a)
OneToOne
chicken
(Gallus gallus)
Aves DENND1B 33 34
  • 75.66 (n)
lizard
(Anolis carolinensis)
Reptilia DENND1B 34
  • 46 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia dennd1b 33
  • 70.27 (n)
zebrafish
(Danio rerio)
Actinopterygii dennd1b 33 34
  • 61.01 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG18659 34
  • 17 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rme-4 34
  • 21 (a)
OneToMany
Species where no ortholog for DENND1B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • wheat (Triticum aestivum)

Evolution for DENND1B Gene

ENSEMBL:
Gene Tree for DENND1B (if available)
TreeFam:
Gene Tree for DENND1B (if available)

Paralogs for DENND1B Gene

(3) SIMAP similar genes for DENND1B Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with DENND1B: view

Variants for DENND1B Gene

Sequence variations from dbSNP and Humsavar for DENND1B Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000024831 -- 197,621,492(+) TACTA(A/C)AAAGA intron-variant
rs1000028489 -- 197,726,604(+) TAATC(A/G)CAGTG intron-variant
rs1000064958 -- 197,575,609(+) ATTAT(A/G)CTACC intron-variant
rs1000067846 -- 197,528,164(+) TAAGT(G/T)TCACA intron-variant
rs1000069461 -- 197,723,353(+) TCTTC(A/G)CACTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for DENND1B Gene

Variant ID Type Subtype PubMed ID
dgv248n106 CNV deletion 24896259
esv1029151 CNV insertion 17803354
esv1218085 CNV deletion 17803354
esv1439856 CNV insertion 17803354
esv2053199 CNV deletion 18987734
esv2558030 CNV deletion 19546169
esv2657002 CNV deletion 23128226
esv2721073 CNV deletion 23290073
esv2721084 CNV deletion 23290073
esv2848458 CNV deletion 24192839
esv3334717 CNV insertion 20981092
esv3544744 CNV deletion 23714750
esv3588502 CNV loss 21293372
esv3588503 CNV loss 21293372
esv3588504 CNV loss 21293372
esv3588506 CNV loss 21293372
esv4662 CNV loss 18987735
esv7266 CNV loss 19470904
esv987539 CNV deletion 20482838
esv992847 CNV deletion 20482838
nsv1068796 CNV deletion 25765185
nsv1125480 CNV tandem duplication 24896259
nsv1137838 CNV deletion 24896259
nsv1159858 CNV duplication 26073780
nsv4010 CNV deletion 18451855
nsv437263 CNV loss 16327808
nsv498702 CNV loss 21111241
nsv511726 CNV loss 21212237
nsv521647 CNV gain 19592680
nsv522400 CNV loss 19592680
nsv548872 CNV loss 21841781
nsv548873 CNV loss 21841781
nsv946566 CNV duplication 23825009
nsv946567 CNV duplication 23825009
nsv952633 CNV duplication 24416366
nsv956505 CNV deletion 24416366

Variation tolerance for DENND1B Gene

Residual Variation Intolerance Score: 17.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.53; 29.64% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for DENND1B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DENND1B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DENND1B Gene

Disorders for DENND1B Gene

MalaCards: The human disease database

(2) MalaCards diseases for DENND1B Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
asthma
  • asthma, protection against
interleukin-7 receptor alpha deficiency
  • il-7r
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

DEN1B_HUMAN
  • Asthma (ASTHMA) [MIM:600807]: The most common chronic disease affecting children and young adults. It is a complex genetic disorder with a heterogeneous phenotype, largely attributed to the interactions among many genes and between these genes and the environment. It is characterized by recurrent attacks of paroxysmal dyspnea, with wheezing due to spasmodic contraction of the bronchi. {ECO:0000269 PubMed:20032318, ECO:0000269 PubMed:26774822}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. Asthma susceptibility is probably caused by decreased TCR down-modulation and recycling in TH2 cells, causing prolonged TCR signaling and increased cytokine production in TH2 lymphocytes (PubMed:26774822). {ECO:0000269 PubMed:26774822}.

Relevant External Links for DENND1B

Genetic Association Database (GAD)
DENND1B
Human Genome Epidemiology (HuGE) Navigator
DENND1B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DENND1B
genes like me logo Genes that share disorders with DENND1B: view

No data available for Genatlas for DENND1B Gene

Publications for DENND1B Gene

  1. Variants of DENND1B associated with asthma in children. (PMID: 20032318) Sleiman PM … Hakonarson H (The New England journal of medicine 2010) 3 4 45 60
  2. Regulation of T Cell Receptor Signaling by DENND1B in TH2 Cells and Allergic Disease. (PMID: 26774822) Yang CW … Chan AC (Cell 2016) 3 4 60
  3. Phosphorylation-dependent Regulation of Connecdenn/DENND1 Guanine Nucleotide Exchange Factors. (PMID: 26055712) Kulasekaran G … McPherson PS (The Journal of biological chemistry 2015) 3 4 60
  4. Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate. (PMID: 22065758) Wu X … Reinisch KM (Proceedings of the National Academy of Sciences of the United States of America 2011) 3 4 60
  5. The connecdenn family, Rab35 guanine nucleotide exchange factors interfacing with the clathrin machinery. (PMID: 20154091) Marat AL … McPherson PS (The Journal of biological chemistry 2010) 3 4 60

Products for DENND1B Gene

Sources for DENND1B Gene

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