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Aliases for BDNF Gene

Aliases for BDNF Gene

  • Brain Derived Neurotrophic Factor 2 3 5
  • Neurotrophin 2 3
  • Abrineurin 3 4
  • Brain-Derived Neurotrophic Factor 3
  • ANON2 3
  • BULN2 3

External Ids for BDNF Gene

Previous GeneCards Identifiers for BDNF Gene

  • GC11P029056
  • GC11M028453
  • GC11M027715
  • GC11M027640
  • GC11M027633
  • GC11M027374
  • GC11M027676

Summaries for BDNF Gene

Entrez Gene Summary for BDNF Gene

  • This gene encodes a member of the nerve growth factor family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature protein. Binding of this protein to its cognate receptor promotes neuronal survival in the adult brain. Expression of this gene is reduced in Alzheimer's, Parkinson's, and Huntington's disease patients. This gene may play a role in the regulation of the stress response and in the biology of mood disorders. [provided by RefSeq, Nov 2015]

GeneCards Summary for BDNF Gene

BDNF (Brain Derived Neurotrophic Factor) is a Protein Coding gene. Diseases associated with BDNF include Central Hypoventilation Syndrome, Congenital and Obsessive-Compulsive Disorder. Among its related pathways are ERK Signaling and Cytoskeleton remodeling Regulation of actin cytoskeleton by Rho GTPases. Gene Ontology (GO) annotations related to this gene include signaling receptor binding and neurotrophin TRKB receptor binding. An important paralog of this gene is NTF3.

UniProtKB/Swiss-Prot for BDNF Gene

  • During development, promotes the survival and differentiation of selected neuronal populations of the peripheral and central nervous systems. Participates in axonal growth, pathfinding and in the modulation of dendritic growth and morphology. Major regulator of synaptic transmission and plasticity at adult synapses in many regions of the CNS. The versatility of BDNF is emphasized by its contribution to a range of adaptive neuronal responses including long-term potentiation (LTP), long-term depression (LTD), certain forms of short-term synaptic plasticity, as well as homeostatic regulation of intrinsic neuronal excitability.

Tocris Summary for BDNF Gene

  • Trk (neurotrophin) receptors are single transmembrane catalytic receptors with intracellular tyrosine kinase activity. Trk receptors are coupled to the Ras, Cdc42/Rac/RhoG, MAPK, PI3K and PLCgamma signaling pathways. Four members of the Trk family have been identified.

Gene Wiki entry for BDNF Gene

Additional gene information for BDNF Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BDNF Gene

Genomics for BDNF Gene

GeneHancer (GH) Regulatory Elements for BDNF Gene

Promoters and enhancers for BDNF 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
GH11J027696 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 661.1 +22.7 22689 6.3 SIN3A GLIS2 ARID2 ZNF143 DEK SP3 REST GLIS1 MYNN NBN BDNF LIN7C GC11P027695 GC11M027675 ENSG00000255496 BDNF-AS
GH11J027717 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE 656.6 +3.3 3295 2.1 PKNOX1 ZSCAN4 SIN3A BMI1 ZNF335 GLIS2 EGR2 CEBPB ZNF398 REST BDNF LIN7C GC11M027675 GC11M027711 GC11P027695 ENSG00000255496
GH11J027721 Enhancer 1 Ensembl ENCODE 650.7 -0.5 -481 1.7 USF1 BACH1 SIN3A ZIC2 ZNF335 ZFHX2 GLIS2 POLR2A PATZ1 ZSCAN5C BDNF LIN7C GC11M027675 GC11M027711 ENSG00000255496
GH11J027720 Enhancer 0.6 ENCODE 650.7 +1.4 1389 0.2 CTCF AFF1 ZNF680 SIN3A MIER2 REST CHAMP1 GLIS2 HDAC2 ZNF143 BDNF GC11M027675 GC11M027711 GC11P027695 ENSG00000255496
GH11J027722 Enhancer 0.6 ENCODE 650.7 +1.6 1619 0.2 CTCF AFF1 ZNF680 SIN3A MIER2 REST CHAMP1 GLIS2 HDAC2 ZNF143 BDNF GC11M027675 GC11M027711 GC11P027695 ENSG00000255496
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BDNF on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BDNF gene promoter:
  • NRSF form 1

Genomic Locations for BDNF Gene

Genomic Locations for BDNF Gene
chr11:27,654,893-27,722,058
(GRCh38/hg38)
Size:
67,166 bases
Orientation:
Minus strand
chr11:27,676,440-27,743,605
(GRCh37/hg19)
Size:
67,166 bases
Orientation:
Minus strand

Genomic View for BDNF Gene

Genes around BDNF on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for BDNF Gene

Proteins for BDNF Gene

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

    Protein Symbol:
    P23560-BDNF_HUMAN
    Recommended name:
    Brain-derived neurotrophic factor
    Protein Accession:
    P23560
    Secondary Accessions:
    • A7LA85
    • A7LA92
    • D3DQZ2
    • Q598Q1
    • Q6DN19
    • Q6YNR2
    • Q6YNR3
    • Q9BYY7
    • Q9UC24

    Protein attributes for BDNF Gene

    Size:
    247 amino acids
    Molecular mass:
    27818 Da
    Quaternary structure:
    • Monomers and homodimers. Binds to NTRK2/TRKB.

    Three dimensional structures from OCA and Proteopedia for BDNF Gene

    Alternative splice isoforms for BDNF Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for BDNF Gene

Post-translational modifications for BDNF Gene

Antibody Products

  • Abcam antibodies for BDNF

No data available for DME Specific Peptides for BDNF Gene

Domains & Families for BDNF Gene

Gene Families for BDNF Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

Graphical View of Domain Structure for InterPro Entry

P23560

UniProtKB/Swiss-Prot:

BDNF_HUMAN :
  • Belongs to the NGF-beta family.
Family:
  • Belongs to the NGF-beta family.
genes like me logo Genes that share domains with BDNF: view

Function for BDNF Gene

Molecular function for BDNF Gene

UniProtKB/Swiss-Prot Function:
During development, promotes the survival and differentiation of selected neuronal populations of the peripheral and central nervous systems. Participates in axonal growth, pathfinding and in the modulation of dendritic growth and morphology. Major regulator of synaptic transmission and plasticity at adult synapses in many regions of the CNS. The versatility of BDNF is emphasized by its contribution to a range of adaptive neuronal responses including long-term potentiation (LTP), long-term depression (LTD), certain forms of short-term synaptic plasticity, as well as homeostatic regulation of intrinsic neuronal excitability.
GENATLAS Biochemistry:
brain-derived neurotrophic factor (neurotrophin 2) ligand for NTRK2 (TRKB),expressed in retina and the anterior segment of the developing eye

LifeMap Function Summary for BDNF Gene

BDNF as growth factor is involved in stem cell differentiation protocols towards the derivation of the following cells:

Phenotypes From GWAS Catalog for BDNF Gene

Gene Ontology (GO) - Molecular Function for BDNF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005169 neurotrophin TRKB receptor binding IBA --
GO:0008083 growth factor activity IBA --
genes like me logo Genes that share ontologies with BDNF: view
genes like me logo Genes that share phenotypes with BDNF: view

Human Phenotype Ontology for BDNF Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for BDNF Gene

MGI Knock Outs for BDNF:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

Clone Products

  • Addgene plasmids for BDNF

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for BDNF Gene

Localization for BDNF Gene

Subcellular locations from UniProtKB/Swiss-Prot for BDNF Gene

Secreted.

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 BDNF gene
Compartment Confidence
extracellular 5
mitochondrion 5
nucleus 5
plasma membrane 3
cytoskeleton 3
endoplasmic reticulum 2
cytosol 2
endosome 2
lysosome 1
golgi apparatus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for BDNF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IBA --
GO:0005615 extracellular space IBA --
GO:0005737 cytoplasm ISS --
GO:0005739 mitochondrion IDA --
GO:0008021 synaptic vesicle IBA --
genes like me logo Genes that share ontologies with BDNF: view

Pathways & Interactions for BDNF Gene

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

SIGNOR curated interactions for BDNF Gene

Activates:

Gene Ontology (GO) - Biological Process for BDNF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway IBA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development TAS 2236018
GO:0007411 axon guidance TAS 19036963
GO:0007416 synapse assembly IDA 19036963
genes like me logo Genes that share ontologies with BDNF: view

Drugs & Compounds for BDNF Gene

(181) Drugs for BDNF Gene - From: DrugBank, PharmGKB, ClinicalTrials, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Citalopram Approved Pharma 526
Dopamine Approved Pharma Full agonist, Agonist 4008
Escitalopram Approved, Investigational Pharma 0
Ethanol Approved Pharma 2326
Fluoxetine Approved, Vet_approved Pharma Channel blocker, Antagonist, Inhibition, Inhibitor 245

(54) Additional Compounds for BDNF Gene - From: Novoseek and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
AG 879
148741-30-4
LM11A 31 dihydrochloride
1243259-19-9

(4) Tocris Compounds for BDNF Gene

Compound Action Cas Number
AG 879 TrkA inhibitor 148741-30-4
BDNF (human) Activates TrkB and p75 receptors 218441-99-7
LM11A 31 dihydrochloride Nonpeptide p75NTR ligand; neuroprotective 1243259-19-9
TLQP 21 VGF-derived peptide 869988-94-3
genes like me logo Genes that share compounds with BDNF: view

Transcripts for BDNF Gene

mRNA/cDNA for BDNF Gene

(19) REFSEQ mRNAs :
(43) Additional mRNA sequences :
(6) Selected AceView cDNA sequences:
(19) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for BDNF Gene

Brain-derived neurotrophic factor:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

Clone Products

  • Addgene plasmids for BDNF

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

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b · 8c · 8d · 8e
SP1: - - - -
SP2: - - -
SP3: - -
SP4: -
SP5: - - - - - - - - -
SP6: - - - - - - - -
SP7: - - - - - - -
SP8: - - - - - -
SP9: - - - - -
SP10:

Relevant External Links for BDNF Gene

GeneLoc Exon Structure for
BDNF
ECgene alternative splicing isoforms for
BDNF

Expression for BDNF Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for BDNF Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x4.1).

Protein differential expression in normal tissues from HIPED for BDNF Gene

This gene is overexpressed in Platelet (41.3) and Peripheral blood mononuclear cells (27.7).

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



Protein tissue co-expression partners for BDNF Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of BDNF Gene:

BDNF

SOURCE GeneReport for Unigene cluster for BDNF Gene:

Hs.502182

mRNA Expression by UniProt/SwissProt for BDNF Gene:

P23560-BDNF_HUMAN
Tissue specificity: Brain. Highly expressed in hippocampus, amygdala, cerebral cortex and cerebellum. Also expressed in heart, lung, skeletal muscle, testis, prostate and placenta.

Evidence on tissue expression from TISSUES for BDNF Gene

  • Nervous system(4.9)
  • Blood(4.6)
  • Adrenal gland(2.8)
  • Eye(2.6)
  • Heart(2.4)
  • Muscle(2.4)
  • Bone marrow(2)
  • Intestine(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for BDNF Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • outer ear
  • skull
  • tooth
Thorax:
  • diaphragm
  • esophagus
  • heart
  • lung
Abdomen:
  • intestine
  • kidney
  • large intestine
  • stomach
Pelvis:
  • penis
  • rectum
  • testicle
  • urethra
General:
  • blood
  • blood vessel
  • peripheral nervous system
  • skin
  • spinal cord
  • sweat gland
genes like me logo Genes that share expression patterns with BDNF: view

Orthologs for BDNF Gene

This gene was present in the common ancestor of chordates.

Orthologs for BDNF Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia BDNF 34 33
  • 99.46 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia BDNF 34
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia BDNF 34 33
  • 93.66 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Bdnf 16 34 33
  • 92.26 (n)
rat
(Rattus norvegicus)
Mammalia Bdnf 33
  • 92.26 (n)
cow
(Bos Taurus)
Mammalia BDNF 34 33
  • 92.17 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia BDNF 34
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves BDNF 34 33
  • 85.91 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia BDNF 34
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia bdnf 33
  • 82.65 (n)
African clawed frog
(Xenopus laevis)
Amphibia bdnf-A 33
zebrafish
(Danio rerio)
Actinopterygii bdnf 34 33 33
  • 76.39 (n)
OneToOne
Species where no ortholog for BDNF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for BDNF Gene

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

Paralogs for BDNF Gene

Paralogs for BDNF Gene

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

  • BDNF_HUMAN
  • E9PMP3_HUMAN
  • Q304R1_HUMAN
  • Q6T2C9_HUMAN
  • Q6YNR1_HUMAN
genes like me logo Genes that share paralogs with BDNF: view

Variants for BDNF Gene

Sequence variations from dbSNP and Humsavar for BDNF Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs6265 risk-factor, protective, benign, Memory impairment, susceptibility to, Obsessive-compulsive disorder, protection against, Anorexia nervosa 2, Bulimia nervosa 2, Bipolar affective disorder, susceptibility to, Parkinson disease, not specified 27,658,369(-) C/T coding_sequence_variant, missense_variant
rs8192466 pathogenic, Congenital central hypoventilation, Congenital central hypoventilation syndrome (CCHS) [MIM:209880] 27,658,560(-) G/A/T coding_sequence_variant, missense_variant
rs2353512 benign, not specified 27,658,115(-) C/T coding_sequence_variant, synonymous_variant
rs66866077 benign, not specified 27,699,390(-) C/A/G/T coding_sequence_variant, genic_upstream_transcript_variant, intron_variant, missense_variant, stop_gained
rs1000040386 -- 27,719,144(-) G/C genic_upstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
nsv1070019 CNV deletion 25765185
nsv1070945 CNV deletion 25765185
nsv474533 CNV novel sequence insertion 20440878
nsv819223 CNV gain 19587683
nsv832095 CNV gain 17160897
nsv951324 CNV deletion 24416366

Variation tolerance for BDNF Gene

Residual Variation Intolerance Score: 39.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.79; 86.77% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BDNF Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for BDNF Gene

MalaCards: The human disease database

(85) MalaCards diseases for BDNF Gene - From: HGMD, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search BDNF in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

BDNF_HUMAN
  • Bulimia nervosa 2 (BULN2) [MIM:610269]: A psychiatric disorder characterized by eating an unusually large amount of food in a short period of time, followed by inappropriate acts (purging) to avert weight gain. Compensatory behavior includes self-induced vomiting, laxative abuse, and excessive exercise. {ECO:0000269 PubMed:15115760}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Congenital central hypoventilation syndrome (CCHS) [MIM:209880]: Rare disorder characterized by abnormal control of respiration in the absence of neuromuscular or lung disease, or an identifiable brain stem lesion. A deficiency in autonomic control of respiration results in inadequate or negligible ventilatory and arousal responses to hypercapnia and hypoxemia. {ECO:0000269 PubMed:11840487}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for BDNF

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

No data available for Genatlas for BDNF Gene

Publications for BDNF Gene

  1. Brain-derived neurotrophic factor and obesity in the WAGR syndrome. (PMID: 18753648) Han JC … Yanovski JA (The New England journal of medicine 2008) 3 4 22 44 58
  2. Brain-derived neurotrophic factor ( BDNF) gene: no major impact on antidepressant treatment response. (PMID: 19236730) Domschke K … Baune BT (The international journal of neuropsychopharmacology 2010) 3 22 44 58
  3. The effect of depression, BDNF gene val66met polymorphism and gender on serum BDNF levels. (PMID: 19589373) Ozan E … Akarsu N (Brain research bulletin 2010) 3 22 44 58
  4. Met carriers of BDNF Val66Met genotype show increased N-acetylaspartate concentration in the anterior cingulate cortex. (PMID: 19683059) Gallinat J … Lang UE (NeuroImage 2010) 3 22 44 58
  5. BDNF Val66Met polymorphism is associated with HPA axis reactivity to psychological stress characterized by genotype and gender interactions. (PMID: 18990498) Shalev I … Kaitz M (Psychoneuroendocrinology 2009) 3 22 44 58

Products for BDNF Gene