BNIP3L
BCL2 interacting protein 3 like
Basic information
Region (hg38): 8:26383054-26505636
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 BNIP3L 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 1 | 0 |
Variants in BNIP3L
This is a list of pathogenic ClinVar variants found in the BNIP3L region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-26383204-C-G | not specified | Uncertain significance (Jan 30, 2024) | ||
| 8-26383213-C-T | not specified | Uncertain significance (Dec 30, 2023) | ||
| 8-26391265-G-A | not specified | Uncertain significance (Jan 31, 2024) | ||
| 8-26391320-G-A | not specified | Uncertain significance (Feb 08, 2023) | ||
| 8-26408055-C-T | not specified | Likely benign (Mar 21, 2022) | ||
| 8-26408298-G-C | not specified | Uncertain significance (Oct 05, 2023) | ||
| 8-26408303-A-T | not specified | Uncertain significance (Feb 01, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BNIP3L | protein_coding | protein_coding | ENST00000380629 | 6 | 122739 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.153 | 0.832 | 125744 | 0 | 4 | 125748 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.18 | 84 | 120 | 0.698 | 0.00000586 | 1460 |
| Missense in Polyphen | 12 | 35.762 | 0.33555 | 472 | ||
| Synonymous | -0.777 | 54 | 47.2 | 1.14 | 0.00000260 | 398 |
| Loss of Function | 2.10 | 3 | 10.2 | 0.293 | 4.32e-7 | 130 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000292 | 0.0000292 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Induces apoptosis. Interacts with viral and cellular anti-apoptosis proteins. Can overcome the suppressors BCL-2 and BCL-XL, although high levels of BCL-XL expression will inhibit apoptosis. Inhibits apoptosis induced by BNIP3. 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. May function as a tumor suppressor. {ECO:0000269|PubMed:10381623, ECO:0000269|PubMed:21264228}.;
- Pathway
- Mitophagy - animal - Homo sapiens (human);Apoptosis;Photodynamic therapy-induced HIF-1 survival signaling;Apoptotic Signaling Pathway;TP53 Regulates Transcription of Cell Death Genes;Gene expression (Transcription);Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;TP53 Regulates Transcription of Genes Involved in Cytochrome C Release;Transcriptional Regulation by TP53;Direct p53 effectors
(Consensus)
Recessive Scores
- pRec
- 0.0976
Intolerance Scores
- loftool
- 0.259
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.729
- hipred
- Y
- hipred_score
- 0.615
- ghis
- 0.587
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bnip3l
- Phenotype
- immune system phenotype; growth/size/body region 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); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- negative regulation of mitochondrial membrane potential;viral process;positive regulation of macroautophagy;mitochondrial protein catabolic process;regulation of apoptotic process;positive regulation of apoptotic process;negative regulation of apoptotic process;defense response to virus;negative regulation of cell death;cellular response to hypoxia;mitochondrial outer membrane permeabilization;regulation of autophagy of mitochondrion;regulation of protein targeting to mitochondrion
- Cellular component
- nuclear envelope;mitochondrion;mitochondrial outer membrane;endoplasmic reticulum;cytosol;integral component of membrane;nuclear speck;intrinsic component of membrane
- Molecular function
- protein binding;lamin binding;identical protein binding;protein homodimerization activity;protein heterodimerization activity