BNIP2

gene
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Also known as Nip2BNIP-2

Summary

BNIP2 (BCL2 interacting protein 2, HGNC:1083) is a protein-coding gene on chromosome 15q22.2, encoding BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 (Q12982). Implicated in the suppression of cell death. It is a selective cancer dependency (DepMap: 13.6% of cell lines).

This gene is a member of the BCL2/adenovirus E1B 19 kd-interacting protein (BNIP) family. It interacts with the E1B 19 kDa protein, which protects cells from virally-induced cell death. The encoded protein also interacts with E1B 19 kDa-like sequences of BCL2, another apoptotic protector. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 663 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 77 total
  • Cancer dependency (DepMap): dependent in 13.6% of screened cell lines
  • MANE Select transcript: NM_004330

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1083
Approved symbolBNIP2
NameBCL2 interacting protein 2
Location15q22.2
Locus typegene with protein product
StatusApproved
AliasesNip2, BNIP-2
Ensembl geneENSG00000140299
Ensembl biotypeprotein_coding
OMIM603292
Entrez663

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 16 protein_coding, 5 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000415213, ENST00000417312, ENST00000439052, ENST00000448414, ENST00000464390, ENST00000477543, ENST00000478981, ENST00000557987, ENST00000560458, ENST00000560776, ENST00000607373, ENST00000897496, ENST00000897497, ENST00000897498, ENST00000897499, ENST00000897500, ENST00000897501, ENST00000897502, ENST00000921900, ENST00000921901, ENST00000921902, ENST00000950838, ENST00000950839, ENST00000950840

RefSeq mRNA: 8 — MANE Select: NM_004330 NM_001320674, NM_001320675, NM_001368057, NM_001368058, NM_001368059, NM_001368060, NM_001368061, NM_004330

CCDS: CCDS10174, CCDS92007

Canonical transcript exons

ENST00000607373 — 10 exons

ExonStartEnd
ENSE000009423175966889259668990
ENSE000013103675968913559689320
ENSE000019230415965914659664120
ENSE000035199125968024159680308
ENSE000035440565967791159678087
ENSE000035851645966927659669362
ENSE000036500545967959259679768
ENSE000036585595967263759672739
ENSE000036931415967118359671314
ENSE000037009035968240859682514

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 99.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 51.6615 / max 1517.2306, expressed in 1823 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
15028551.66151823

Top tissues by expression

296 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370199.03gold quality
monocyteCL:000057698.10gold quality
mononuclear cellCL:000084297.90gold quality
leukocyteCL:000073897.74gold quality
colonic epitheliumUBERON:000039796.97gold quality
bone marrow cellCL:000209296.76gold quality
rectumUBERON:000105296.52gold quality
body of pancreasUBERON:000115096.24gold quality
bone marrowUBERON:000237195.99gold quality
minor salivary glandUBERON:000183095.43gold quality
adrenal tissueUBERON:001830395.30gold quality
right uterine tubeUBERON:000130295.22gold quality
right lungUBERON:000216795.09gold quality
tendonUBERON:000004394.99gold quality
gall bladderUBERON:000211094.91gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099194.46gold quality
omental fat padUBERON:001041494.44gold quality
peritoneumUBERON:000235894.42gold quality
left lobe of thyroid glandUBERON:000112094.41gold quality
metanephros cortexUBERON:001053394.35gold quality
subcutaneous adipose tissueUBERON:000219094.31gold quality
adipose tissue of abdominal regionUBERON:000780894.30gold quality
olfactory segment of nasal mucosaUBERON:000538694.24gold quality
upper lobe of left lungUBERON:000895294.20gold quality
vermiform appendixUBERON:000115494.16gold quality
mouth mucosaUBERON:000372994.09gold quality
upper lobe of lungUBERON:000894893.99gold quality
transverse colonUBERON:000115793.96gold quality
thyroid glandUBERON:000204693.94gold quality
small intestine Peyer’s patchUBERON:000345493.92gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

234 targeting BNIP2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3646100.0073.565283
HSA-MIR-5692A100.0074.406850
HSA-MIR-4682100.0068.891258
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-656-3P100.0072.152788
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-548AW99.9972.573559
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-366299.9973.825684
HSA-MIR-453199.9969.703181
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-1213699.9872.815713
HSA-MIR-477599.9875.006394
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-480399.9871.993117
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-314899.9775.066478
HSA-MIR-60799.9773.625593
HSA-MIR-807599.9767.20962

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 13.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 11)

  • Transfection of the bnip2 cDNA in neuroblastoma cell line results in massive cell death counteracted by Bcl-2 overexpression; bnip2 is the mediator of the anti-apoptotic activity of estrogens in a variety of cells (PMID:11744098)
  • BNIPL-2, a novel homologue of BNIP-2, interacts with Bcl-2 and Cdc42GAP in apoptosis. (PMID:12901880)
  • BNIP-2 has a role in regulating cell dynamics with a novel Rho GTPase-activating protein, BPGAP1 (PMID:12944407)
  • BNIP-2 in vivo induces cell dynamics by recruiting Cdc42 (PMID:15652341)
  • Our results suggest that the caspase-mediated cleavage of BNIP-2 and BNIP-XL could result in the release of the BCH domain or smaller fragments that are crucial for their proapoptotic activities. (PMID:17961507)
  • Inhibition of BNIP-2 expression did not affect the susceptibility to NK cell-mediated killing. (PMID:20704564)
  • Data imply that SIRT1 may mediate MPP(+)-induced cytotoxicity, possibly through the regulation of BNIP2. (PMID:21130087)
  • BNIP-2 directly interacted with the motor and tail domains of KIF5B via its BCH domain. (PMID:25378581)
  • BNIP-2 is a kinesin-1 adapter involved in vesicular transportation in the cytoplasm and that association with cargos depends on interaction of the CRAL-TRIO domain with membrane phosphatidylserine. (PMID:25472445)
  • BNIP-2 retards breast cancer cell migration by coupling microtubule-mediated GEF-H1 and RhoA activation. (PMID:32789168)
  • BNIP-2 Activation of Cellular Contractility Inactivates YAP for H9c2 Cardiomyoblast Differentiation. (PMID:35975420)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriobnip2ENSDARG00000013397
mus_musculusBnip2ENSMUSG00000011958
rattus_norvegicusBnip2ENSRNOG00000056024
drosophila_melanogasterCG11593FBGN0035488

Paralogs (3): PRUNE2 (ENSG00000106772), BNIPL (ENSG00000163141), ATCAY (ENSG00000167654)

Protein

Protein identifiers

BCL2/adenovirus E1B 19 kDa protein-interacting protein 2Q12982 (reviewed: Q12982)

All UniProt accessions (3): Q12982, H7C096, H7C142

UniProt curated annotations — full annotation on UniProt →

Function. Implicated in the suppression of cell death. Interacts with the BCL-2 and adenovirus E1B 19 kDa proteins.

Subcellular location. Cytoplasm. Perinuclear region.

Isoforms (2)

UniProt IDNamesCanonical?
Q12982-11yes
Q12982-22

RefSeq proteins (8): NP_001307603, NP_001307604, NP_001354986, NP_001354987, NP_001354988, NP_001354989, NP_001354990, NP_004321* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001251CRAL-TRIO_domDomain
IPR022181Bcl2-/adenovirus-E1BFamily
IPR036865CRAL-TRIO_dom_sfHomologous_superfamily

Pfam: PF12496, PF13716

UniProt features (14 total): modified residue 6, region of interest 2, chain 1, domain 1, splice variant 1, sequence variant 1, sequence conflict 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q12982-F173.060.37

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (6): 114, 41, 77, 87, 89, 92

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-525793Myogenesis
R-HSA-1266738Developmental Biology

MSigDB gene sets: 265 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, HORIUCHI_WTAP_TARGETS_DN, GNF2_BNIP2, HOFMANN_CELL_LYMPHOMA_UP, GCANCTGNY_MYOD_Q6, GOBP_POSITIVE_REGULATION_OF_NEURON_DIFFERENTIATION, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_POSITIVE_REGULATION_OF_MAPK_CASCADE, GENTILE_RESPONSE_CLUSTER_D3, GOBP_NEUROGENESIS, CAGCTG_AP4_Q5, GOCC_MICROTUBULE_ORGANIZING_CENTER

GO Biological Process (9): blastocyst development (GO:0001824), apoptotic process (GO:0006915), centrosome cycle (GO:0007098), negative regulation of apoptotic process (GO:0043066), positive regulation of MAPK cascade (GO:0043410), positive regulation of neuron differentiation (GO:0045666), positive regulation of small GTPase mediated signal transduction (GO:0051057), striated muscle cell differentiation (GO:0051146), response to oxygen-glucose deprivation (GO:0090649)

GO Molecular Function (3): GTPase activator activity (GO:0005096), calcium ion binding (GO:0005509), protein binding (GO:0005515)

GO Cellular Component (8): nuclear envelope (GO:0005635), nucleolus (GO:0005730), cytoplasm (GO:0005737), centriole (GO:0005814), cytosol (GO:0005829), spindle pole centrosome (GO:0031616), intracellular membrane-bounded organelle (GO:0043231), perinuclear region of cytoplasm (GO:0048471)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Developmental Biology1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
positive regulation of intracellular signal transduction2
intracellular membraneless organelle2
intracellular anatomical structure2
cytoplasm2
in utero embryonic development1
anatomical structure development1
programmed cell death1
apoptotic signaling pathway1
execution phase of apoptosis1
cell cycle process1
microtubule organizing center organization1
apoptotic process1
regulation of apoptotic process1
negative regulation of programmed cell death1
MAPK cascade1
regulation of MAPK cascade1
neuron differentiation1
positive regulation of cell differentiation1
regulation of neuron differentiation1
small GTPase-mediated signal transduction1
regulation of small GTPase mediated signal transduction1
muscle cell differentiation1
response to nutrient levels1
response to decreased oxygen levels1
GTPase activity1
enzyme activator activity1
GTPase regulator activity1
metal ion binding1
binding1
nucleus1
endomembrane system1
organelle envelope1
nuclear lumen1
microtubule organizing center1
spindle pole1
centrosome1
membrane-bounded organelle1
intracellular organelle1

Protein interactions and networks

STRING

1518 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BNIP2BCL2P10415955
BNIP2BNIP1Q12981885
BNIP2BNIP3Q12983882
BNIP2TTPAP49638736
BNIP2ARHGAP1Q07960717
BNIP2CDC42P21181688
BNIP2PRR5P85299678
BNIP2PRUNE1Q86TP1632
BNIP2NIP7Q9Y221506
BNIP2CALB1P05937504
BNIP2APPL1Q9UKG1496
BNIP2ARHGEF1Q92888454
BNIP2TAX1BP3O14907447
BNIP2GEMIN6Q8WXD5447
BNIP2GCNT3O95395437

IntAct

163 interactions, top by confidence:

ABTypeScore
FRKBNIP2psi-mi:“MI:0915”(physical association)0.830
BNIP2FRKpsi-mi:“MI:0915”(physical association)0.830
FATE1BNIP2psi-mi:“MI:0915”(physical association)0.720
BNIP2psi-mi:“MI:0915”(physical association)0.560
BNIP2KLC1psi-mi:“MI:0915”(physical association)0.560
MYO5BBNIP2psi-mi:“MI:0915”(physical association)0.560
BNIP2MYO5Bpsi-mi:“MI:0915”(physical association)0.560
BNIP2psi-mi:“MI:0915”(physical association)0.560
KLC1BNIP2psi-mi:“MI:0915”(physical association)0.560
BNIP2SIN3Apsi-mi:“MI:0915”(physical association)0.560
BNIP2ABHD4psi-mi:“MI:0915”(physical association)0.560
BNIP2TMX2psi-mi:“MI:0915”(physical association)0.560
BNIP2GRAMD2Apsi-mi:“MI:0915”(physical association)0.560

BioGRID (94): FRK (Two-hybrid), KLC1 (Two-hybrid), MYO5B (Two-hybrid), UPK1B (Two-hybrid), FATE1 (Two-hybrid), BNIP2 (Affinity Capture-RNA), BNIP2 (Affinity Capture-RNA), CREB3 (Two-hybrid), BNIP2 (Two-hybrid), BNIP2 (Two-hybrid), BNIP2 (Proximity Label-MS), BNIP2 (Two-hybrid), ARHGAP1 (FRET), BNIP2 (Affinity Capture-MS), BNIP2 (Two-hybrid)

ESM2 similar proteins: A1L0Y5, A5PJU9, A7T167, B2RR83, P08487, P10686, P19174, P42209, P49846, P56523, P87141, Q03606, Q0IHU9, Q0VC68, Q12982, Q14BI7, Q15019, Q16KN5, Q22307, Q24087, Q292F9, Q29JQ0, Q2NKY7, Q3MHU3, Q4V8H8, Q5BKN4, Q5E9R3, Q5EB96, Q5R746, Q5RA66, Q62077, Q63ZQ1, Q6C2J1, Q6NU25, Q7JUR6, Q8BH64, Q8NDG6, Q8S6N5, Q99719, Q9BGQ3

Diamond homologs: O54940, P85298, Q07960, Q0IHU9, Q12982, Q1M168, Q52KR3, Q54TH9, Q55AR6, Q5BJR4, Q5FWK3, Q5R4Q8, Q7Z465, Q86WG3, Q8BHE3, Q8WUY3, Q99JU7, Q9CXP4, Q9GKT0, Q9VTU3, A4IF90, A6NI28, A7T167, B2RQE8, B2RTY4, B2RWW0, B9VTT2, D3ZFJ3, D3ZZN9, E7EZG2, E7F3F0, F1LQX4, O14014, O43182, O54834, O94988, P34288, P35688, P42331, P55194

SIGNOR signaling

2 interactions.

AEffectBMechanism
BNIP2“up-regulates activity”CDC42binding
CDON“up-regulates activity”BNIP2binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

77 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance64
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1525 predictions. Top by Δscore:

VariantEffectΔscore
15:59664119:CT:Cacceptor_gain1.0000
15:59664121:C:CCacceptor_gain1.0000
15:59664137:A:Cacceptor_gain1.0000
15:59668890:A:ACdonor_gain1.0000
15:59668891:C:CTdonor_gain1.0000
15:59668891:CTG:Cdonor_gain1.0000
15:59668891:CTGTT:Cdonor_gain1.0000
15:59671208:T:Adonor_gain1.0000
15:59672629:ATAC:Adonor_loss1.0000
15:59672630:TACTT:Tdonor_loss1.0000
15:59672631:ACT:Adonor_loss1.0000
15:59672632:CTTAC:Cdonor_loss1.0000
15:59672633:TT:Tdonor_loss1.0000
15:59672634:TACTT:Tdonor_loss1.0000
15:59672635:A:ACdonor_gain1.0000
15:59672635:ACTT:Adonor_loss1.0000
15:59672636:C:Adonor_loss1.0000
15:59672636:C:CCdonor_gain1.0000
15:59672636:CTT:Cdonor_gain1.0000
15:59672736:TATC:Tacceptor_gain1.0000
15:59672737:ATCCT:Aacceptor_loss1.0000
15:59672738:TC:Tacceptor_gain1.0000
15:59672738:TCCTA:Tacceptor_loss1.0000
15:59672739:CC:Cacceptor_gain1.0000
15:59672739:CCTA:Cacceptor_loss1.0000
15:59672740:C:CAacceptor_loss1.0000
15:59672740:C:CCacceptor_gain1.0000
15:59672741:T:Cacceptor_loss1.0000
15:59677909:AC:Adonor_gain1.0000
15:59677909:ACCC:Adonor_gain1.0000

AlphaMissense

2084 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:59668943:A:GL281P1.000
15:59668973:T:AK271I1.000
15:59668981:G:CF268L1.000
15:59668981:G:TF268L1.000
15:59668982:A:GF268S1.000
15:59668983:A:GF268L1.000
15:59669294:A:TV259D1.000
15:59669333:A:TI246N1.000
15:59669339:A:GL244P1.000
15:59669348:A:GL241P1.000
15:59669353:T:AK239N1.000
15:59669353:T:GK239N1.000
15:59669354:T:AK239I1.000
15:59671215:C:AW225C1.000
15:59671215:C:GW225C1.000
15:59671217:A:GW225R1.000
15:59671217:A:TW225R1.000
15:59671264:A:TV209D1.000
15:59672643:A:GL190P1.000
15:59672685:G:TP176H1.000
15:59668972:T:AK271N0.999
15:59668972:T:GK271N0.999
15:59668974:T:CK271E0.999
15:59668982:A:CF268C0.999
15:59668984:T:AK267N0.999
15:59668984:T:GK267N0.999
15:59668985:T:AK267I0.999
15:59668986:T:CK267E0.999
15:59669279:A:TI264N0.999
15:59669282:A:GF263S0.999

dbSNP variants (sampled 300 via entrez): RS1000015947 (15:59687688 C>T), RS1000030061 (15:59666425 G>C,T), RS1000066852 (15:59678209 A>C,T), RS1000219851 (15:59685447 G>A,C), RS1000409896 (15:59675977 A>T), RS1000439350 (15:59681189 C>T), RS1000643456 (15:59662200 C>G), RS1000733460 (15:59689536 C>G,T), RS1000819003 (15:59672839 T>C), RS1001294641 (15:59683111 T>C), RS1001376824 (15:59688132 G>A), RS1001433762 (15:59668045 T>A,C), RS1001480413 (15:59687715 C>G,T), RS1001620568 (15:59675437 T>C), RS1001719413 (15:59665165 G>C)

Disease associations

OMIM: gene MIM:603292 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST003875_16Gut microbiota (bacterial taxa)4.000000e-11
GCST003875_17Gut microbiota (bacterial taxa)4.000000e-11

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007874gut microbiome measurement
EFO:0007883taxonomic microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Resveratrolaffects cotreatment, increases expression2
Estradiolaffects expression, decreases expression2
Valproic Acidaffects expression, increases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
methylmercuric chlorideincreases expression1
bisphenol Aincreases expression1
VX-agentincreases expression1
beta-lapachoneincreases expression1
sodium arseniteincreases expression1
cobaltous chlorideincreases expression1
casticindecreases expression1
K 7174increases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
bisphenol Sdecreases methylation1
jinfukangdecreases expression1
brevetoxin 2decreases expression1
PCI 5002increases expression, affects cotreatment1
Sunitinibincreases expression1
Fulvestrantincreases methylation1
Leflunomideincreases expression1
Bexarotenedecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arbutinincreases expression1
Atrazinedecreases expression1
Benzo(a)pyreneaffects methylation1
Caffeineincreases phosphorylation1
Capsaicinincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.