This gene is encodes a mitochondrial protein that contains a BH3 domain and acts as a pro-apoptotic factor. The encoded protein interacts with anti-apoptotic proteins, including the E1B 19 kDa protein and Bcl2. This gene is silenced in tumors by DNA methylation. [provided by RefSeq, Dec 2014] See more...

Aliases for BNIP3 Gene

Aliases for BNIP3 Gene

  • BCL2 Interacting Protein 3 2 3 5
  • BCL2/Adenovirus E1B 19 KDa Protein-Interacting Protein 3 3 4
  • BCL2/Adenovirus E1B 19kDa Interacting Protein 3 2 3
  • Nineteen KD Interacting Protein-3 2 3
  • NIP3 3 4
  • BCL2/Adenovirus E1B Interacting Protein 3 3
  • BNIP3 5
  • Nip3 2

External Ids for BNIP3 Gene

Previous GeneCards Identifiers for BNIP3 Gene

  • GC14U990005
  • GC14P026723
  • GC10M133215
  • GC10M133631
  • GC10M133781
  • GC10M127330

Summaries for BNIP3 Gene

Entrez Gene Summary for BNIP3 Gene

  • This gene is encodes a mitochondrial protein that contains a BH3 domain and acts as a pro-apoptotic factor. The encoded protein interacts with anti-apoptotic proteins, including the E1B 19 kDa protein and Bcl2. This gene is silenced in tumors by DNA methylation. [provided by RefSeq, Dec 2014]

GeneCards Summary for BNIP3 Gene

BNIP3 (BCL2 Interacting Protein 3) is a Protein Coding gene. Diseases associated with BNIP3 include Hereditary Leiomyomatosis And Renal Cell Cancer and Leiomyomatosis. Among its related pathways are Apoptosis Modulation and Signaling and Shigellosis. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and protein heterodimerization activity. An important paralog of this gene is BNIP3L.

UniProtKB/Swiss-Prot Summary for BNIP3 Gene

  • Apoptosis-inducing protein that can overcome BCL2 suppression. May play a role in repartitioning calcium between the two major intracellular calcium stores in association with BCL2. Involved in mitochondrial quality control via its interaction with SPATA18/MIEAP: in response to mitochondrial damage, participates in mitochondrial protein catabolic process (also named MALM) leading to the degradation of damaged proteins inside mitochondria. The physical interaction of SPATA18/MIEAP, BNIP3 and BNIP3L/NIX at the mitochondrial outer membrane regulates the opening of a pore in the mitochondrial double membrane in order to mediate the translocation of lysosomal proteins from the cytoplasm to the mitochondrial matrix. Plays an important role in the calprotectin (S100A8/A9)-induced cell death pathway.

Gene Wiki entry for BNIP3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for BNIP3 Gene

Genomics for BNIP3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for BNIP3 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
GH10J131977 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 250.7 +1.0 1025 6.8 TBP SP1 BHLHE40 NONO ZIC2 THAP11 REST FOXA2 MAX VEZF1 BNIP3 ENSG00000273521 lnc-PPP2R2D-2 PPP2R2D
GH10J132036 Promoter/Enhancer 0.9 Ensembl dbSUPER 11.2 -54.6 -54588 1.2 ZIC2 CTCF GLIS1 ZFP69B L3MBTL2 ZBTB8A EZH2 ZNF692 ZFX GLIS2 JAKMIP3 BNIP3 HSALNG0081749 piR-58852-006 DPYSL4
GH10J132008 Enhancer 0.5 Ensembl 17.8 -28.5 -28488 3.4 MAFF ZNF316 MAFK MAFG ATF2 CEBPB NANOG EMSY BNIP3 piR-48348-006 HSALNG0081749 JAKMIP3 lnc-PPP2R2D-2
GH10J132096 Enhancer 0.9 Ensembl ENCODE 10.2 -113.8 -113787 2.4 CEBPA ZIC2 MAX SMAD4 SAP130 ZNF341 ETV4 RARA JUND TCF7L2 BNIP3 ENSG00000235010 piR-48553-050 HSALNG0081750 JAKMIP3 DPYSL4
GH10J132005 Enhancer 0.7 Ensembl 12.2 -23.2 -23186 0.4 ELF1 TAF9B ZNF316 NFE2 MAFG MEIS2 GABPB1 NR2C1 DPF2 PTTG1 piR-48348-006 piR-49097-014 JAKMIP3 BNIP3 ENSG00000279982 lnc-PPP2R2D-6 lnc-PPP2R2D-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around BNIP3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for BNIP3

Top Transcription factor binding sites by QIAGEN in the BNIP3 gene promoter:
  • AML1a
  • ATF-2
  • GR
  • GR-alpha
  • GR-beta
  • HNF-1
  • p53

Genomic Locations for BNIP3 Gene

Latest Assembly
chr10:131,966,455-131,982,013
(GRCh38/hg38)
Size:
15,559 bases
Orientation:
Minus strand

Previous Assembly
chr10:133,781,187-133,795,517
(GRCh37/hg19 by Entrez Gene)
Size:
14,331 bases
Orientation:
Minus strand

chr10:133,781,578-133,795,435
(GRCh37/hg19 by Ensembl)
Size:
13,858 bases
Orientation:
Minus strand

Genomic View for BNIP3 Gene

Genes around BNIP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
BNIP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for BNIP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for BNIP3 Gene

Proteins for BNIP3 Gene

  • Protein details for BNIP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q12983-BNIP3_HUMAN
    Recommended name:
    BCL2/adenovirus E1B 19 kDa protein-interacting protein 3
    Protein Accession:
    Q12983
    Secondary Accessions:
    • O14620
    • Q96GP0

    Protein attributes for BNIP3 Gene

    Size:
    259 amino acids
    Molecular mass:
    27832 Da
    Quaternary structure:
    • Homodimer. Binds to BCL2. Interacts with BNIP3L and ACAA2. Interacts (via BH3 domain) with SPATA18 (via coiled-coil domains). Interacts with BOK; promotes BOK oligomerization (PubMed:15868100).
    • (Microbial infection) Interacts with adenovirus E1B 19 kDa protein.
    • (Microbial infection) Interacts with Epstein-Barr virus BHRF1.
    SequenceCaution:
    • Sequence=AAC00022.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAC16738.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAH21989.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=AAW62256.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for BNIP3 Gene

neXtProt entry for BNIP3 Gene

Post-translational modifications for BNIP3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for BNIP3 Gene

Antibodies for research

  • Abcam antibodies for BNIP3

No data available for DME Specific Peptides for BNIP3 Gene

Domains & Families for BNIP3 Gene

Gene Families for BNIP3 Gene

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

Protein Domains for BNIP3 Gene

InterPro:
Blocks:
  • BNIP3
ProtoNet:

Suggested Antigen Peptide Sequences for BNIP3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60537, highly similar to BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 (B4DHJ7_HUMAN)
  • BCL2/adenovirus E1B 19 kDa protein-interacting protein 3 (BNIP3_HUMAN)
  • BNIP3 protein (Q66K24_HUMAN)
  • BNIP3 protein (Q6NVY4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q12983

UniProtKB/Swiss-Prot:

BNIP3_HUMAN :
  • Belongs to the NIP3 family.
Family:
  • Belongs to the NIP3 family.
genes like me logo Genes that share domains with BNIP3: view

Function for BNIP3 Gene

Molecular function for BNIP3 Gene

UniProtKB/Swiss-Prot Function:
Apoptosis-inducing protein that can overcome BCL2 suppression. May play a role in repartitioning calcium between the two major intracellular calcium stores in association with BCL2. Involved in mitochondrial quality control via its interaction with SPATA18/MIEAP: in response to mitochondrial damage, participates in mitochondrial protein catabolic process (also named MALM) leading to the degradation of damaged proteins inside mitochondria. The physical interaction of SPATA18/MIEAP, BNIP3 and BNIP3L/NIX at the mitochondrial outer membrane regulates the opening of a pore in the mitochondrial double membrane in order to mediate the translocation of lysosomal proteins from the cytoplasm to the mitochondrial matrix. Plays an important role in the calprotectin (S100A8/A9)-induced cell death pathway.

Phenotypes From GWAS Catalog for BNIP3 Gene

Gene Ontology (GO) - Molecular Function for BNIP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 7954800
GO:0042802 identical protein binding IEA,IPI 10381623
GO:0042803 protein homodimerization activity IDA 9396766
GO:0051020 GTPase binding IPI 20436456
genes like me logo Genes that share ontologies with BNIP3: view
genes like me logo Genes that share phenotypes with BNIP3: view

Animal Models for BNIP3 Gene

MGI Knock Outs for BNIP3:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for BNIP3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for BNIP3 Gene

Localization for BNIP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for BNIP3 Gene

Mitochondrion. Mitochondrion outer membrane. Single-pass membrane protein. Note=Coexpression with the EIB 19-kDa protein results in a shift in NIP3 localization pattern to the nuclear envelope. Colocalizes with ACAA2 in the mitochondria. Colocalizes with SPATA18 at the mitochondrion outer membrane.

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 BNIP3 gene
Compartment Confidence
mitochondrion 5
nucleus 5
endoplasmic reticulum 4
cytosol 4
lysosome 3
plasma membrane 2
extracellular 2
cytoskeleton 2
peroxisome 2
endosome 2
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for BNIP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,ISS --
GO:0005635 nuclear envelope IBA,IDA 7954800
GO:0005654 nucleoplasm IEA,ISS --
GO:0005737 cytoplasm IEA,ISS --
GO:0005739 mitochondrion IEA,TAS 9973195
genes like me logo Genes that share ontologies with BNIP3: view

Pathways & Interactions for BNIP3 Gene

genes like me logo Genes that share pathways with BNIP3: view

Pathways by source for BNIP3 Gene

SIGNOR curated interactions for BNIP3 Gene

Inactivates:

Gene Ontology (GO) - Biological Process for BNIP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000422 autophagy of mitochondrion NAS 22505714
GO:0001666 response to hypoxia IEA,ISS --
GO:0006915 apoptotic process IPI 7954800
GO:0008219 cell death IEA,ISS --
GO:0009617 response to bacterium IEA --
genes like me logo Genes that share ontologies with BNIP3: view

Drugs & Compounds for BNIP3 Gene

(9) Drugs for BNIP3 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6876

(8) Additional Compounds for BNIP3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with BNIP3: view

Transcripts for BNIP3 Gene

mRNA/cDNA for BNIP3 Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
4 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 BNIP3

Alternative Splicing Database (ASD) splice patterns (SP) for BNIP3 Gene

No ASD Table

Relevant External Links for BNIP3 Gene

GeneLoc Exon Structure for
BNIP3

Expression for BNIP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for BNIP3 Gene

mRNA differential expression in normal tissues according to GTEx for BNIP3 Gene

This gene is overexpressed in Pancreas (x7.0).

Protein differential expression in normal tissues from HIPED for BNIP3 Gene

This gene is overexpressed in Frontal cortex (19.6), CD4 Tcells (15.0), Heart (8.2), Pancreas (6.1), and Liver (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for BNIP3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for BNIP3

SOURCE GeneReport for Unigene cluster for BNIP3 Gene:

Hs.144873

Evidence on tissue expression from TISSUES for BNIP3 Gene

  • Nervous system(4.8)
  • Liver(4.7)
  • Muscle(3.4)
  • Heart(3.3)
  • Kidney(3)
  • Blood(2.8)
  • Pancreas(2.8)
  • Intestine(2.7)
  • Lung(2.6)
  • Skin(2.5)
  • Spleen(2.3)
  • Adrenal gland(2.1)
genes like me logo Genes that share expression patterns with BNIP3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for BNIP3 Gene

Orthologs for BNIP3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for BNIP3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia BNIP3 30 31
  • 98.8 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia BNIP3 31
  • 94 (a)
OneToOne
LOC607408 30
  • 87.29 (n)
Rat
(Rattus norvegicus)
Mammalia Bnip3 30
  • 90.2 (n)
Mouse
(Mus musculus)
Mammalia Bnip3 30 17 31
  • 90.02 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia BNIP3 30 31
  • 83.33 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia BNIP3 31
  • 75 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia BNIP3 31
  • 64 (a)
OneToOne
Chicken
(Gallus gallus)
Aves BNIP3 30 31
  • 78.08 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia BNIP3 31
  • 74 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia bnip3 30
  • 74.27 (n)
Str.2462 30
African clawed frog
(Xenopus laevis)
Amphibia MGC68574 30
Zebrafish
(Danio rerio)
Actinopterygii bnip3 30 31
  • 69.43 (n)
OneToMany
bnip4 31
  • 42 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.3722 31
  • 26 (a)
OneToMany
Species where no ortholog for BNIP3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 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)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for BNIP3 Gene

ENSEMBL:
Gene Tree for BNIP3 (if available)
TreeFam:
Gene Tree for BNIP3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for BNIP3: view image

Paralogs for BNIP3 Gene

Paralogs for BNIP3 Gene

(1) SIMAP similar genes for BNIP3 Gene using alignment to 4 proteins:

  • BNIP3_HUMAN
  • B4DHJ7_HUMAN
  • Q66K24_HUMAN
  • Q6NVY4_HUMAN
genes like me logo Genes that share paralogs with BNIP3: view

Variants for BNIP3 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for BNIP3 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 BNIP3 Gene

Variant ID Type Subtype PubMed ID
esv3577861 CNV gain 25503493
esv3624956 CNV gain 21293372
nsv1054934 CNV gain 25217958
nsv825650 CNV gain 20364138
nsv825651 CNV gain 20364138

Variation tolerance for BNIP3 Gene

Residual Variation Intolerance Score: 53.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.68; 14.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BNIP3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
BNIP3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for BNIP3 Gene

Disorders for BNIP3 Gene

MalaCards: The human disease database

(11) MalaCards diseases for BNIP3 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
hereditary leiomyomatosis and renal cell cancer
  • hlrcc
leiomyomatosis
legionellosis
  • legionella infection
adrenal gland pheochromocytoma
  • pheochromocytoma
neuronal ceroid lipofuscinosis
  • hereditary ceroid lipofuscinosis
- elite association - COSMIC cancer census association via MalaCards
Search BNIP3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for BNIP3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 BNIP3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for BNIP3 Gene

Publications for BNIP3 Gene

  1. S100A8/A9 induces autophagy and apoptosis via ROS-mediated cross-talk between mitochondria and lysosomes that involves BNIP3. (PMID: 19935772) Ghavami S … Los M (Cell research 2010) 3 4 23
  2. Acetyl-Coenzyme A acyltransferase 2 attenuates the apoptotic effects of BNIP3 in two human cell lines. (PMID: 18371312) Cao W … Lu H (Biochimica et biophysica acta 2008) 3 4 23
  3. Adenovirus E1B-19K/BCL-2 interacting protein BNIP3 contains a BH3 domain and a mitochondrial targeting sequence. (PMID: 9575197) Yasuda M … Chinnadurai G (The Journal of biological chemistry 1998) 3 4 23
  4. Adenovirus E1B 19 kDa and Bcl-2 proteins interact with a common set of cellular proteins. (PMID: 7954800) Boyd JM … Chinnadurai G (Cell 1994) 2 3 4
  5. BNIP3 and NIX mediate Mieap-induced accumulation of lysosomal proteins within mitochondria. (PMID: 22292033) Nakamura Y … Arakawa H (PloS one 2012) 3 4

Products for BNIP3 Gene

  • Addgene plasmids for BNIP3

Sources for BNIP3 Gene