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Atlas / Gene / BNIP2

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
  • GTEx eGene: eQTL in 19 tissues, sQTL in 12 (q < 0.05)
  • Cancer dependency (DepMap): dependent in 13.6% of screened cell lines
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.05 (unconstrained)
  • MANE Select transcript: NM_004330
  • Notable: 77 clinical variants but no curated precision-oncology (CIViC) evidence yet

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: 30 — 21 protein_coding, 5 retained_intron, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

MANE Select: ENST00000607373

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 5, TSL 3: 3, TSL 5: 2

ENST00000607373, ENST00000415213, ENST00000417312, ENST00000439052, ENST00000448414, ENST00000464390, ENST00000477543, ENST00000478981, ENST00000557987, ENST00000560458, ENST00000560776, ENST00000897496, ENST00000897497, ENST00000897498, ENST00000897499, ENST00000897500, ENST00000897501, ENST00000897502, ENST00000921900, ENST00000921901, ENST00000921902, ENST00000950838, ENST00000950839, ENST00000950840, ENST00000973446, ENST00001045172, ENST00001045173, ENST00001045174, ENST00001112641, ENST00001112642

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.

Highest expression (Bgee): calcaneal tendon, monocyte, mononuclear cell, leukocyte, colonic epithelium.

Genetic regulation across tissues (GTEx eQTL / sQTL)

BNIP2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 19 tissues and its splicing (sQTL) in 12 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 31 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Cells EBV-transformed lymphocytessqtl8.0e-31+0.9215:59687970:G:T
Brain Cerebellumeqtl4.0e-15+0.3315:59671896:T:A
Brain Cerebellar Hemisphereeqtl7.9e-13+0.2715:59708040:G:C
Adipose Subcutaneoussqtl2.0e-12-0.3315:59668742:CCT:C
Adipose Visceral Omentumsqtl2.7e-09+0.4115:59683451:T:C
Artery Tibialeqtl1.2e-08-0.1115:59652101:T:C
Thyroidsqtl1.3e-08+0.4015:59640937:T:TC
Cells EBV-transformed lymphocyteseqtl6.6e-07+0.6115:59663325:C:G
Muscle Skeletaleqtl2.0e-06+0.0915:59691500:T:C
Cells Cultured fibroblastseqtl3.4e-06+0.3515:59666938:C:CT
Testiseqtl4.3e-05-0.0915:59654562:T:C
Whole Bloodsqtl7.6e-05-0.3315:59668062:T:C
Lungsqtl1.7e-04+0.3415:59686710:C:G
Whole Bloodeqtl3.4e-04-0.0415:59691500:T:C
Thyroideqtl4.9e-04-0.0915:59659798:C:A
Breast Mammary Tissuesqtl5.5e-04+0.2215:59638932:A:G
Esophagus Mucosaeqtl6.8e-04-0.1315:59692683:C:G
Skin Sun Exposed Lower legsqtl1.0e-03-0.3015:59662524:T:A
Pancreaseqtl1.3e-03+0.1815:59688514:G:GAC
Spleensqtl5.0e-03-0.4915:59715485:T:C

FANTOM5 promoters

1 alternative TSS:

Promoter IDTPM avgSamples expressed
15028551.66151823

Top tissues by expression

showing 100 of 296 tissues 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
bloodUBERON:000017893.90gold quality
left ventricle myocardiumUBERON:000656693.82gold quality
right lobe of thyroid glandUBERON:000111993.81gold quality
adipose tissueUBERON:000101393.76gold quality
granulocyteCL:000009493.73gold quality
mucosa of stomachUBERON:000119993.71gold quality
connective tissueUBERON:000238493.70gold quality
tibial arteryUBERON:000761093.64gold quality
popliteal arteryUBERON:000225093.62gold quality
superficial temporal arteryUBERON:000161493.39gold quality
lungUBERON:000204893.39gold quality
seminal vesicleUBERON:000099893.36gold quality
epithelium of nasopharynxUBERON:000195193.34gold quality
germinal epithelium of ovaryUBERON:000130493.32gold quality
aortaUBERON:000094793.28gold quality
pancreasUBERON:000126493.27gold quality
lymph nodeUBERON:000002993.21gold quality
descending thoracic aortaUBERON:000234593.16gold quality
left uterine tubeUBERON:000130393.15gold quality
left coronary arteryUBERON:000162693.09gold quality
body of stomachUBERON:000116193.03gold quality
gastrocnemiusUBERON:000138893.02gold quality
small intestineUBERON:000210893.02gold quality
muscle of legUBERON:000138392.95gold quality
cardiac muscle of right atriumUBERON:000337992.91gold quality
vaginaUBERON:000099692.86gold quality
thoracic aortaUBERON:000151592.86gold quality
right lobe of liverUBERON:000111492.83gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450292.81gold quality
ascending aortaUBERON:000149692.78gold quality
tibial nerveUBERON:000132392.77gold quality
cardiac atriumUBERON:000208192.65gold quality
right atrium auricular regionUBERON:000663192.64gold quality
endocervixUBERON:000045892.63gold quality
stromal cell of endometriumCL:000225592.62gold quality
coronary arteryUBERON:000162192.59gold quality
saliva-secreting glandUBERON:000104492.56gold quality
caecumUBERON:000115392.56gold quality
heartUBERON:000094892.52gold quality
spleenUBERON:000210692.51gold quality
myocardiumUBERON:000234992.48gold quality
urinary bladderUBERON:000125592.47gold quality
hindlimb stylopod muscleUBERON:000425292.43gold quality
right coronary arteryUBERON:000162592.42gold quality
ectocervixUBERON:001224992.40gold quality
skin of abdomenUBERON:000141692.39gold quality
thoracic mammary glandUBERON:000520092.36gold quality
heart left ventricleUBERON:000208492.35gold quality
mammary glandUBERON:000191192.33gold quality
stomachUBERON:000094592.31gold quality
layer of synovial tissueUBERON:000761692.30gold quality
cardiac ventricleUBERON:000208292.28gold quality
cauda epididymisUBERON:000436092.27gold quality
lower esophagus mucosaUBERON:003583492.20gold quality
parietal pleuraUBERON:000240092.13gold quality
esophagus mucosaUBERON:000246992.12gold quality
tonsilUBERON:000237292.08gold quality
esophagusUBERON:000104392.05gold quality
heart right ventricleUBERON:000208092.00gold quality
visceral pleuraUBERON:000240192.00gold quality
pleuraUBERON:000097791.99gold quality
endometriumUBERON:000129591.95gold quality
left adrenal gland cortexUBERON:003582591.94gold quality
esophagogastric junction muscularis propriaUBERON:003584191.94gold quality
biceps brachiiUBERON:000150791.91gold quality
lower esophagusUBERON:001347391.89gold quality
skeletal muscle organUBERON:001489291.89gold quality
muscle organUBERON:000163091.88gold quality
lower esophagus muscularis layerUBERON:003583391.88gold quality
muscle layer of sigmoid colonUBERON:003580591.86gold quality

Single-cell (SCXA)

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

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

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Bone marrowtissue122.0high
Tonsiltissue43.4high
Lymph nodetissue42.5high
Adipose tissuetissue41.3medium
Livertissue41.0low
Thymustissue40.4
Spleentissue39.0medium
Heart muscletissue38.0low
Placentatissue37.9high
Appendixtissue36.4low
Urinary bladdertissue36.3medium
Tonguetissue36.3
Smooth muscletissue36.1low
Lungtissue34.9high
Endometrium 1tissue32.6not detected
Skeletal muscletissue30.2low
Ovarytissue27.1low
Breasttissue27.0medium
Esophagustissue26.4medium
Seminal vesicletissue25.9not detected
Cervixtissue25.0low
Retinatissue23.8
Prostatetissue23.3not detected
Gallbladdertissue23.1medium
Frontal cortextissue20.8
Septumtissue20.5
Hypothalamustissue20.3
Testistissue20.1medium
Nucleus accumbenstissue20.1
Caudate putamentissue20.1
Spinal cordtissue19.8
Rectumtissue19.7not detected
Adrenal glandtissue19.7medium
Hippocampustissue18.8low
Corpus callosumtissue18.8
Amygdalatissue18.3
Cerebellumtissue18.2low
Locus coeruleustissue18.1
Periaqueductal graytissue18.0
Olfactory bulbtissue17.9
Skin 1tissue17.8medium
Choroid plexustissue17.5
Midbraintissue17.5
Substantia nigratissue17.4
Colontissue17.3low
Small intestinetissue17.2not detected
Ventral forebraintissue17.2
Epididymistissue16.6not detected
Hippocampal formationtissue16.6
Putamentissue16.5
Cerebral cortextissue16.2low
Retrosplenial and cingulate cortextissue16.2
Medulla oblongatatissue16.1
Kidneytissue16.1medium
Fallopian tubetissue16.1not detected
Insular cortextissue16.1
Basal gangliatissue16.0not detected
Ponstissue15.9
Retrosplenial cortextissue15.7
Prefrontal cortextissue15.5

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Area postrema (29.7), Cerebellar white matter (29.4), Cervical spinal cord, ventral horn (29.1), Supraoptic nucleus (29.1), Medial olivary nucleus (28.6).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting BNIP2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 234 miRNAs:

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

gnomAD constraint: pLI 9.47e-08, LOEUF 1.05, missense Z -1.1 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000607373 — one region, missense o/e 1.11. DepMap (CRISPR cell-line fitness): dependent in 13.6% of screened cell lines.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): NCI-H1155 (-1.201), AM-38 (-0.888), GB-1 (-0.838), KYSE-510 (-0.827), HPAF-II (-0.815), 23132/87 (-0.814), D-542MG (-0.812), UWB1.289 (-0.788), KYSE-410 (-0.785), HCC1143 (-0.758), MFM-223 (-0.75), SNU-81 (-0.731), KYSE-70 (-0.725), SK-GT-4 (-0.715), SF-295 (-0.71).

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)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:109327) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 8 distinct phenotype terms.

Mouse phenotype (MP)Records
abnormal cranium morphology1
abnormal tibia morphology1
abnormal femur morphology1
decreased erythrocyte cell number1
increased circulating alkaline phosphatase level1
increased lean body mass1
increased mean corpuscular hemoglobin1
abnormal incisor color1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Pongo abeliiQ5R4Q899.1%Diamond
Macaca fascicularisQ9GKT098.4%Diamond
Xenopus tropicalisQ5CZL191.7%Diamond
Dictyostelium discoideumQ55AR633.8%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
GTF2A2protein-coding2958
GCNT3protein-coding9245
FOXB1protein-coding27023

Protein

Protein identifiers

BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 — Q12982 (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

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q12982-F173.060.37

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; nucleoli

Antibody reliability (HPA): IH approved · IF supported

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)

TypePositions
Phosphoserine114, 41, 77, 89, 92
Phosphothreonine87

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 2; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

2 pathways:

IDPathwayEvidence
R-HSA-1266738Developmental Biology—
R-HSA-525793Myogenesiselectronic

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 (3): apoptotic process (GO:0006915), negative regulation of apoptotic process (GO:0043066), 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 (7): nuclear envelope (GO:0005635), 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

1 top-level categories:

CategoryPathways
Developmental Biology1

GO top-level categories

25 GO namespaces:

CategoryTerms
cellular anatomical structure3
intracellular anatomical structure2
cytoplasm2
programmed cell death1
apoptotic signaling pathway1
execution phase of apoptosis1
apoptotic process1
regulation of apoptotic process1
negative regulation of programmed cell death1
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
microtubule organizing center1
intracellular membraneless organelle1
spindle pole1
centrosome1
membrane-bounded organelle1
intracellular organelle1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 4 of 13 annotations. The rest are phylogenetic / computational / electronic (IEA).

4 experimentally-supported GO terms:

GO termNSEvidence
cytoplasmCCdirect assay
cytosolCCdirect assay
intracellular membrane-bounded organelleCCdirect assay
nuclear envelopeCCdirect assay

Protein interactions and networks

STRING

showing 16 of 794 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
BNIP2BNIP1Q12981882
BNIP2BNIP3Q12983874
BNIP2TTPAP49638735
BNIP2PRR5P85299672
BNIP2BCL2P10415652
BNIP2PRUNE1Q86TP1631
BNIP2CALB1P05937520
BNIP2TAX1BP3O14907469
BNIP2NIP7Q9Y221461
BNIP2GCNT3O95395456
BNIP2GEMIN6Q8WXD5404
BNIP2ANXA5P08758399
BNIP2CRADDP78560382
BNIP2ARHGAP8P85298375
BNIP2ENSAO43768370
BNIP2DBNLP84070370

IntAct

Human interaction partners of BNIP2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

showing 30 of 51 partners by confidence:

PartnerInteraction typeMIscoreRecords
FRKphysical association0.8308
FATE1physical association0.7206
MYO5Bphysical association0.5608
KLC1physical association0.5606
ABHD4physical association0.5603
AGPAT3physical association0.5603
APOBEC3Bphysical association0.5603
BNIP3physical association0.5603
BNIP5physical association0.5603
CHODLphysical association0.5603
CPLX4physical association0.5603
CYB5R3physical association0.5603
DESI2physical association0.5603
DGAT2L6physical association0.5603
DHRS1physical association0.5603
EI24physical association0.5603
ERLIN1physical association0.5603
FAHD1physical association0.5603
FAM209Aphysical association0.5603
FAM3Cphysical association0.5603
GORABphysical association0.5603
GPR152physical association0.5603
GPX8physical association0.5603
GRAMD2Aphysical association0.5603
GSC2physical association0.5603
KCNK5physical association0.5603
LDLRAD1physical association0.5603
LIME1physical association0.5603
MEOX1physical association0.5603
MEOX2physical association0.5603

BioGRID (94 interactions; top human partners by supporting records): ARHGAP1 (FRET; 6 records), CDC42 (Reconstituted Complex; 5 records), BCL2 (Two-hybrid; 3 records), FRK (Two-hybrid; 3 records), ATG16L1 (Proximity Label-MS; 2 records), FATE1 (Two-hybrid; 2 records), KLC1 (Two-hybrid; 2 records), MYO5B (Two-hybrid; 2 records), RAB11A (Proximity Label-MS; 2 records), ABHD4 (Two-hybrid), AGPAT3 (Two-hybrid), APOBEC3B (Two-hybrid), ATG9A (Proximity Label-MS), BNIP3 (Two-hybrid), BNIPL (Two-hybrid)

SIGNOR signaling

2 signaling interactions:

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

Protein complexes (CORUM) (1)

Experimentally-characterized complexes this protein is a subunit of (★ = the complex contains a known drug target).

1 complexes by size:

ComplexSubunitsMembers
BNIP2-ARHGAP8 complex2ARHGAP8, BNIP2

Disease & clinical

Genetic variants

Variant evidence for BNIP2: 77 ClinVar records (0 pathogenic / likely pathogenic); 2 GWAS associations.

ClinVar

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

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

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 37 predictions of 861):

Position(s)EffectΔscoreSites
15:59671208donor_gain1.0000
15:59672635–59672636donor_loss1.00005
15:59672740–59672741acceptor_loss1.00006
15:59678088–59678089acceptor_loss1.00005
15:59679590–59679591donor_loss1.00005
15:59679594donor_gain1.0000
15:59679769–59679770acceptor_loss1.00004
15:59679775acceptor_gain1.0000
15:59680239–59680240donor_loss1.00005
15:59680309–59680310acceptor_loss1.00004

AlphaMissense

960 missense substitutions predicted likely pathogenic (of 2,084 scored), across 198 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
M18790.9380.996
F26880.9951.000
H24880.9940.999
H15680.9890.998
F17080.9880.999
F19180.9850.999
F26380.9830.999
S26580.9810.994
D14380.9730.995
N24080.9690.997
D23480.9490.995
F25280.9450.996
D1280.8790.976
M22080.8720.980
D9980.8440.970
D30080.8330.960
W22570.9981.000
C17370.9860.998
K27170.9851.000
M17570.9840.996

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

CancerPrognosticp-value
Pancreatic Adenocarcinoma (validation)unfavorable8.63e-05
Kidney Renal Clear Cell Carcinoma (TCGA)favorable0.000164

Disease associations

OMIM: gene MIM:603292 | disease phenotypes:

GWAS associations

2 associations:

StudyTraitp-value
GCST003875_5Gut microbiota (bacterial taxa)4e-11
GCST003875_6Gut microbiota (bacterial taxa)4e-11

EFO canonical traits (from GWAS)

2 canonical traits:

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

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

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 5002affects cotreatment, increases expression1
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)

Via MONDO — disease-level, not drug-specific.

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

About this page

Built deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source. Provided for research and reference, not medical advice or a diagnosis. Data may be incomplete, especially for rare conditions. Consult a qualified clinician.

Generated
Atlas version
v1.12.2
BioBTree
v2.16.1

Sources 94

This page pulls from 94 datasets indexed by BioBTree:

alliance_phenotypealphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruscellphonedbchembl_activitychembl_mechanismchembl_moleculechembl_targetciviccivic_assertioncivic_evidencecivic_variantclingen_dosageclingen_gene_validityclingen_variantclinical_trialsclinvarcollectricorumctd_gene_interactiondepmapdepmap_dependencydiamond_similarityefoensemblentrezexonfantom5_genefantom5_promotergenccgenerifgnomad_constraintgnomad_rmcgogoparentgtex_egenegtopdbgwasgwas_studyhgnchpahpa_expressionhpa_pathologyhpointactinterprointogenjasparmeshmgimimmirdbmondomsigdbneighborentrezorphanetorthologorthologentrezpanelapp_geneparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_var_annotationpharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontaxonomytranscriptufeatureuniprot