BNIP5

Summary

BNIP5 (BCL2 interacting protein 5, HGNC:33769) is a protein-coding gene on chromosome 6p21.31, encoding Protein BNIP5 (P0C671).

At a glance

• Clinical variants (ClinVar): 13 total — 1 pathogenic
• MANE Select transcript: NM_001010903

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33769
Approved symbol	BNIP5
Name	BCL2 interacting protein 5
Location	6p21.31
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp779B1540
Ensembl gene	ENSG00000189325
Ensembl biotype	protein_coding
Entrez	389384

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000437635, ENST00000860604, ENST00000860605, ENST00000860606, ENST00000860607, ENST00000944763

RefSeq mRNA: 1 — MANE Select: NM_001010903 NM_001010903

CCDS: CCDS34439

Canonical transcript exons

ENST00000437635 — 12 exons

Exon	Start	End
ENSE00001365346	36326510	36326753
ENSE00001366989	36323293	36323533
ENSE00001367047	36328598	36328714
ENSE00001369582	36330081	36330694
ENSE00001372436	36327030	36327094
ENSE00001372773	36319356	36319610
ENSE00001375819	36321155	36321219
ENSE00001378518	36325283	36325414
ENSE00001381532	36322311	36322442
ENSE00001384840	36324129	36324190
ENSE00001414120	36336712	36336888
ENSE00001642151	36315761	36317391

Expression profiles

Bgee: expression breadth broad, 43 present calls, max score 89.31.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1290 / max 62.7075, expressed in 26 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
73339	0.1290	26

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
duodenum	UBERON:0002114	89.31	gold quality
islet of Langerhans	UBERON:0000006	80.13	gold quality
mucosa of transverse colon	UBERON:0004991	76.68	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.66	gold quality
rectum	UBERON:0001052	75.43	gold quality
small intestine	UBERON:0002108	70.32	gold quality
small intestine Peyer’s patch	UBERON:0003454	68.97	gold quality
transverse colon	UBERON:0001157	64.01	gold quality
gall bladder	UBERON:0002110	62.89	gold quality
pancreas	UBERON:0001264	62.87	gold quality
body of stomach	UBERON:0001161	59.42	gold quality
stomach	UBERON:0000945	57.75	gold quality
intestine	UBERON:0000160	57.27	gold quality
colonic epithelium	UBERON:0000397	57.14	gold quality
body of pancreas	UBERON:0001150	54.39	gold quality
colon	UBERON:0001155	52.28	gold quality
vermiform appendix	UBERON:0001154	51.35	gold quality
mucosa of stomach	UBERON:0001199	47.05	gold quality
right testis	UBERON:0004534	45.22	gold quality
prefrontal cortex	UBERON:0000451	44.91	silver quality
bone marrow cell	CL:0002092	43.70	gold quality
testis	UBERON:0000473	43.24	gold quality
fundus of stomach	UBERON:0001160	43.20	gold quality
left testis	UBERON:0004533	43.10	gold quality
superior frontal gyrus	UBERON:0002661	42.35	gold quality
smooth muscle tissue	UBERON:0001135	41.89	gold quality
skin of leg	UBERON:0001511	41.18	gold quality
zone of skin	UBERON:0000014	40.90	gold quality
skin of abdomen	UBERON:0001416	40.36	silver quality
frontal cortex	UBERON:0001870	40.11	silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.86
E-GEOD-83139	no	2.84

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

75 targeting BNIP5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-219A-5P	99.91	73.36	735
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-4782-3P	99.88	73.31	735
HSA-MIR-6766-3P	99.88	73.38	732
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-139-5P	99.80	69.50	1399
HSA-MIR-3913-5P	99.78	67.26	968
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-1825	99.72	68.11	1089
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-1303	99.65	69.77	1662
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-1252-3P	99.55	67.71	2862

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Bnip5	ENSMUSG00000048905
rattus_norvegicus	Bnip5	ENSRNOG00000016997

Protein

Protein identifiers

Protein BNIP5 — P0C671 (reviewed: P0C671)

All UniProt accessions (1): P0C671

RefSeq proteins (1): NP_001010903* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031362	BNIP5	Family

Pfam: PF15661

UniProt features (20 total): compositionally biased region 11, region of interest 3, sequence conflict 2, chain 1, cross-link 1, sequence variant 1, helix 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
8IGC	X-RAY DIFFRACTION	1.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0C671-F1	47.88	0.00

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 (1): 302

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): ATGCTGG_MIR338, GTCAGGA_MIR378, FEVR_CTNNB1_TARGETS_UP, ZNF362_TARGET_GENES, MIR548AJ_3P_MIR548X_3P, MIR548AH_3P_MIR548AM_3P, MIR4251, MIR205_5P, MIR1202, MIR3972, GSE13229_IMM_VS_MATURE_NKCELL_UP, MIR519E_3P, MIR515_3P, MIR33B_3P, MIR3158_3P

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

426 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BNIP5	GAGE12H	A6NDE8	571
BNIP5	AVEN	Q9NQS1	468
BNIP5	PXT1	Q8NFP0	419
BNIP5	GOLGA6A	Q9NYA3	418
BNIP5	FAM180B	Q6P0A1	418
BNIP5	HIPK4	Q8NE63	409
BNIP5	C17orf99	Q6UX52	372
BNIP5	BNIP1	Q12981	370
BNIP5	OTUD6A	Q7L8S5	368
BNIP5	DUSP28	Q4G0W2	342
BNIP5	API5	Q9BZZ5	330
BNIP5	C19orf18	Q8NEA5	323
BNIP5	MRPL41	Q8IXM3	322
BNIP5	DAD1	P46966	316
BNIP5	LAMTOR5	O43504	307
BNIP5	ALPG	P10696	307

IntAct

17 interactions, top by confidence:

A	B	Type	Score
BNIP5	MAPK9	psi-mi:“MI:0915”(physical association)	0.670
BNIP5	BCL2L1	psi-mi:“MI:0915”(physical association)	0.560
BNIP5	BCL2L2	psi-mi:“MI:0915”(physical association)	0.560
BNIP5	BNIP2	psi-mi:“MI:0915”(physical association)	0.560
BNIP5	CAPRIN1	psi-mi:“MI:0915”(physical association)	0.400
BNIP5	TCOF1	psi-mi:“MI:0915”(physical association)	0.400
BNIP5	GNPAT	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350
BCL2L2	BNIP5	psi-mi:“MI:0915”(physical association)	0.000
MAPK9	BNIP5	psi-mi:“MI:0915”(physical association)	0.000
BNIP2	BNIP5	psi-mi:“MI:0915”(physical association)	0.000
BCL2L1	BNIP5	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (31): C6orf222 (Two-hybrid), C6orf222 (Two-hybrid), C6orf222 (Two-hybrid), C6orf222 (Two-hybrid), TCOF1 (Proximity Label-MS), CAPRIN1 (Proximity Label-MS), MTHFR (Affinity Capture-MS), ANKRD17 (Affinity Capture-MS), MAPK8 (Affinity Capture-MS), DCAF16 (Affinity Capture-MS), ANAPC4 (Affinity Capture-MS), TBC1D17 (Affinity Capture-MS), GRPEL1 (Affinity Capture-MS), USP7 (Affinity Capture-MS), PDLIM5 (Affinity Capture-MS)

ESM2 similar proteins: A0A0J9YXV3, A0A172M4N0, A2VE23, A5PL33, C7EMF5, E7EW31, F1NSM7, I3L273, O15027, O48582, O55189, O55196, O97939, P0C671, P0DV77, P14138, Q14D33, Q1XI13, Q28989, Q3B7M4, Q4R729, Q5R7U0, Q5SWP3, Q62840, Q63003, Q6E0U4, Q6H236, Q6NUN9, Q6UXA7, Q7Z2K8, Q86UU5, Q8BM15, Q8K4E0, Q8K4L6, Q8N1P7, Q8N3D4, Q96D09, Q96JG9, Q9BGL9, Q9D7G9

Diamond homologs: P0C671, Q8CC96

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	4
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2685202	GRCh37/hg19 6p21.31-21.1(chr6:35562152-42003452)x1	Pathogenic

SpliceAI

1513 predictions. Top by Δscore:

Variant	Effect	Δscore
6:36319405:AGG:A	donor_gain	1.0000
6:36319405:AGGC:A	donor_gain	1.0000
6:36321152:CACCT:C	donor_loss	1.0000
6:36321153:A:AC	donor_gain	1.0000
6:36321154:C:CC	donor_gain	1.0000
6:36321154:CCT:C	donor_gain	1.0000
6:36321154:CCTG:C	donor_gain	1.0000
6:36321215:CTCCT:C	acceptor_gain	1.0000
6:36321216:TCCT:T	acceptor_gain	1.0000
6:36321217:CCTC:C	acceptor_gain	1.0000
6:36321218:CT:C	acceptor_gain	1.0000
6:36321220:C:CC	acceptor_gain	1.0000
6:36321221:T:C	acceptor_loss	1.0000
6:36322305:A:AC	donor_gain	1.0000
6:36322306:C:CC	donor_gain	1.0000
6:36322309:A:AC	donor_gain	1.0000
6:36322310:C:CC	donor_gain	1.0000
6:36322310:CTAG:C	donor_gain	1.0000
6:36322332:G:C	donor_gain	1.0000
6:36323532:TG:T	acceptor_gain	1.0000
6:36323534:C:CC	acceptor_gain	1.0000
6:36324122:T:TA	donor_gain	1.0000
6:36324124:CTCA:C	donor_loss	1.0000
6:36324125:TCA:T	donor_loss	1.0000
6:36324126:CA:C	donor_loss	1.0000
6:36324127:ACCT:A	donor_gain	1.0000
6:36324128:C:CA	donor_loss	1.0000
6:36324128:CCTC:C	donor_gain	1.0000
6:36324130:T:TA	donor_gain	1.0000
6:36324186:TTCTT:T	acceptor_gain	1.0000

AlphaMissense

4282 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:36324183:G:C	F392L	0.971
6:36324183:G:T	F392L	0.971
6:36324185:A:G	F392L	0.971
6:36319609:A:G	I557T	0.952
6:36321186:A:G	L546P	0.939
6:36324184:A:G	F392S	0.936
6:36327061:A:G	L254P	0.932
6:36321198:A:G	L542P	0.929
6:36319609:A:C	I557S	0.928
6:36327061:A:T	L254H	0.927
6:36319546:A:G	L578P	0.923
6:36321186:A:T	L546H	0.913
6:36319587:C:A	K564N	0.910
6:36319587:C:G	K564N	0.910
6:36321198:A:T	L542H	0.909
6:36323435:A:C	F443L	0.909
6:36323435:A:T	F443L	0.909
6:36323437:A:G	F443L	0.909
6:36330396:A:G	W99R	0.902
6:36330396:A:T	W99R	0.902
6:36319555:A:G	L575P	0.897
6:36323426:C:A	K446N	0.887
6:36323426:C:G	K446N	0.887
6:36326559:A:C	F329L	0.887
6:36326559:A:T	F329L	0.887
6:36326561:A:G	F329L	0.887
6:36321186:A:C	L546R	0.877
6:36319534:A:G	L582P	0.875
6:36319593:G:C	S562R	0.873
6:36319593:G:T	S562R	0.873

dbSNP variants (sampled 300 via entrez): RS1000135192 (6:36338824 C>G), RS1000248396 (6:36326806 A>G), RS1000512093 (6:36315837 C>G), RS1000640586 (6:36321973 G>T), RS1000803532 (6:36330827 T>G), RS1000945079 (6:36315538 GC>G), RS1000957673 (6:36318837 A>G), RS1001013403 (6:36319228 A>T), RS1001177814 (6:36318586 G>C), RS1001223243 (6:36321302 C>T), RS1001223660 (6:36318776 G>C), RS1001254868 (6:36325020 G>A,C), RS1001372203 (6:36327384 G>A), RS1001768091 (6:36333996 G>A), RS1002000953 (6:36315931 C>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): prostate cancer (MONDO:0008315)

Orphanet (1): Familial prostate cancer (Orphanet:1331)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D011471	Prostatic Neoplasms	C04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
bisphenol A	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
abrine	increases expression	1
Zoledronic Acid	increases expression	1
Doxorubicin	decreases expression	1
Lipopolysaccharides	increases expression, affects response to substance	1
Rotenone	decreases expression	1
Tobacco Smoke Pollution	affects expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00029224	PHASE4	COMPLETED	Treatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997	PHASE4	COMPLETED	Open-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609	PHASE4	COMPLETED	The Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623	PHASE4	SUSPENDED	The Plenaxis® Experience Study
NCT00106392	PHASE4	COMPLETED	A Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029	PHASE4	UNKNOWN	MR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485	PHASE4	COMPLETED	Angelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219	PHASE4	COMPLETED	Zoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271	PHASE4	COMPLETED	Effect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146	PHASE4	COMPLETED	Study to Evaluate Zoledronic Acid on Quality of Life and Skeletal-related Events as Adjuvant Treatment in Patients With Hormone-naïve Prostate Cancer and Bone Metastasis Who Have Undergone Orchiectomy
NCT00242554	PHASE4	COMPLETED	Open-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098	PHASE4	COMPLETED	Docetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696	PHASE4	COMPLETED	Casodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139	PHASE4	COMPLETED	Effect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765	PHASE4	COMPLETED	Effects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690	PHASE4	COMPLETED	Evaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708	PHASE4	COMPLETED	Local Anesthesia for Prostate Biopsy
NCT00526331	PHASE4	COMPLETED	Evaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213	PHASE4	COMPLETED	Compare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330	PHASE4	TERMINATED	Dissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966	PHASE4	COMPLETED	Radical Prostatectomy and Perioperative Fluid Therapy
NCT00805701	PHASE4	COMPLETED	Study Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027	PHASE4	COMPLETED	Effect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269	PHASE4	UNKNOWN	Can Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277	PHASE4	COMPLETED	Study of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800	PHASE4	COMPLETED	Does Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199	PHASE4	COMPLETED	Global Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226	PHASE4	COMPLETED	Evaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563	PHASE4	COMPLETED	Randomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905	PHASE4	COMPLETED	Study to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672	PHASE4	COMPLETED	3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143	PHASE4	TERMINATED	Prospective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742	PHASE4	UNKNOWN	Comparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563	PHASE4	COMPLETED	Hydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874	PHASE4	COMPLETED	Efficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472	PHASE4	TERMINATED	Firmagon (Degarelix) Intermittent Therapy
NCT01547416	PHASE4	COMPLETED	The Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544	PHASE4	COMPLETED	The Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749	PHASE4	UNKNOWN	Evaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635	PHASE4	COMPLETED	Study of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer