BNIP3
BCL2 interacting protein 3, the group of BCL2 homology region 3 (BH3) only
Basic information
Region (hg38): 10:131967684-131981967
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BNIP3 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 0 |
Variants in BNIP3
This is a list of pathogenic ClinVar variants found in the BNIP3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-131970648-T-C | not specified | Uncertain significance (Jul 14, 2021) | ||
| 10-131970653-A-G | not specified | Uncertain significance (Oct 26, 2022) | ||
| 10-131970718-T-A | not specified | Uncertain significance (Dec 13, 2022) | ||
| 10-131970723-T-G | not specified | Uncertain significance (May 30, 2023) | ||
| 10-131970729-C-T | not specified | Uncertain significance (Feb 22, 2025) | ||
| 10-131970787-C-A | not specified | Uncertain significance (Aug 22, 2023) | ||
| 10-131970873-A-G | not specified | Uncertain significance (Feb 03, 2022) | ||
| 10-131970954-A-G | not specified | Uncertain significance (Jul 13, 2021) | ||
| 10-131973062-T-C | not specified | Uncertain significance (Jul 11, 2023) | ||
| 10-131973065-G-A | not specified | Uncertain significance (Apr 04, 2024) | ||
| 10-131973087-T-C | not specified | Uncertain significance (Oct 26, 2022) | ||
| 10-131973110-C-T | not specified | Uncertain significance (Oct 07, 2024) | ||
| 10-131973111-G-A | not specified | Uncertain significance (Nov 07, 2024) | ||
| 10-131973821-T-C | not specified | Uncertain significance (Mar 01, 2023) | ||
| 10-131981784-C-A | not specified | Uncertain significance (Feb 03, 2025) | ||
| 10-131981785-C-T | not specified | Uncertain significance (Mar 17, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BNIP3 | protein_coding | protein_coding | ENST00000368636 | 6 | 13858 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000197 | 0.482 | 125730 | 0 | 18 | 125748 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.827 | 90 | 115 | 0.783 | 0.00000670 | 1283 |
| Missense in Polyphen | 29 | 45.196 | 0.64166 | 503 | ||
| Synonymous | 0.304 | 41 | 43.6 | 0.941 | 0.00000279 | 357 |
| Loss of Function | 0.534 | 8 | 9.80 | 0.816 | 4.16e-7 | 120 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000995 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000968 | 0.0000967 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- 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. {ECO:0000269|PubMed:19935772, ECO:0000269|PubMed:22292033}.;
- Pathway
- Legionellosis - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Mitophagy - animal - Homo sapiens (human);Busulfan Pathway, Pharmacodynamics;Apoptosis Modulation and Signaling;Photodynamic therapy-induced HIF-1 survival signaling;mTOR signaling pathway;HIF-1-alpha transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.310
Intolerance Scores
- loftool
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.19
Haploinsufficiency Scores
- pHI
- 0.171
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.451
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.970
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bnip3
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype;
Gene ontology
- Biological process
- autophagy of mitochondrion;response to hypoxia;apoptotic process;cell death;granzyme-mediated apoptotic signaling pathway;response to bacterium;positive regulation of autophagy;negative regulation of mitochondrial fusion;cardiac muscle cell apoptotic process;positive regulation of cardiac muscle cell apoptotic process;negative regulation of mitochondrial membrane potential;positive regulation of necrotic cell death;viral process;positive regulation of macroautophagy;cerebral cortex development;mitochondrial protein catabolic process;positive regulation of apoptotic process;negative regulation of apoptotic process;positive regulation of programmed cell death;positive regulation of protein complex disassembly;mitochondrial fragmentation involved in apoptotic process;negative regulation of membrane potential;regulation of mitochondrial membrane permeability;autophagic cell death;oligodendrocyte differentiation;brown fat cell differentiation;neuron apoptotic process;positive regulation of mitochondrial calcium ion concentration;defense response to virus;response to hyperoxia;negative regulation of cell death;cellular response to hydrogen peroxide;cellular response to mechanical stimulus;cellular response to cobalt ion;cellular response to hypoxia;reactive oxygen species metabolic process;positive regulation of mitochondrial fission;positive regulation of release of cytochrome c from mitochondria;mitochondrial outer membrane permeabilization;toxin transport;negative regulation of mitochondrial membrane permeability involved in apoptotic process;positive regulation of autophagy of mitochondrion;regulation of aerobic respiration;intrinsic apoptotic signaling pathway in response to hypoxia;negative regulation of reactive oxygen species metabolic process
- Cellular component
- nucleus;nuclear envelope;nucleoplasm;cytoplasm;mitochondrion;mitochondrial outer membrane;endoplasmic reticulum;postsynaptic density;dendrite;integral component of mitochondrial outer membrane;mitochondrial membrane
- Molecular function
- protein binding;identical protein binding;protein homodimerization activity;protein heterodimerization activity;GTPase binding