BNIP1
protein-codingBCL2 interacting protein 1, the group of BCL2 homology region 3 (BH3) only|SNAREs
Gene summary
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. In addition, this protein is involved in vesicle transport into the endoplasmic reticulum. Alternative splicing of this gene results in four protein products with identical N- and C-termini. [provided by RefSeq, Mar 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~19.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0100510
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BNIP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001205.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 43 | 43 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 49 | 0 | 0 | 49 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001196.2 | 6 | MANE Select | |
| Ensembl | ENSP00000239215.7 | 6 | MANE Select | |
| RefSeq | NP_053581.2 | 5 | Standard | |
| RefSeq | NP_053582.2 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- SNARE interactions in vesicular transport - Homo sapiens (human)
- Vesicle-mediated transport
- Membrane Trafficking
- COPI-dependent Golgi-to-ER retrograde traffic
- Golgi-to-ER retrograde transport
Biological Process
- retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
- apoptotic process
- endoplasmic reticulum organization
- endoplasmic reticulum membrane fusion
- negative regulation of apoptotic process
Molecular Function
- SNAP receptor activity
- protein binding
Cellular Component
- nuclear envelope
- cytoplasm
- endoplasmic reticulum
- endoplasmic reticulum membrane
- integral component of endoplasmic reticulum membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000231668
- Coding exons
- 7
- Length
- 19946
- Individuals with no LoFs
- 125600
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 147
- Defined
- 125747
- p
- 0.000585
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.467 | 130 | 146 | 0.891 | 0.00000768 | 1773 |
| Missense (PolyPhen) | 47 | 47.295 | 0.99377 | 561 | ||
| Synonymous | -1.95 | 74 | 55.5 | 1.33 | 0.00000290 | 517 |
| Loss of Function | 0.877 | 11 | 14.6 | 0.752 | 7.12e-7 | 168 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00029 | 0.00026 | rare |
| Ashkenazi Jewish | 0.0041 | 0.0041 | notable |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0.00029 | 0.00028 | rare |
| European (Non-Finnish) | 0.00058 | 0.00057 | rare |
| South Asian | 0.00026 | 0.00023 | rare |
| Other | 0.0016 | 0.0016 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: As part of a SNARE complex may be involved in endoplasmic reticulum membranes fusion and be required for the maintenance of endoplasmic reticulum organization (PubMed:15272311). Plays also a role in apoptosis (PubMed:7954800, PubMed:15272311, PubMed:23896122). It is for instance required for endoplasmic reticulum stress-induced apoptosis (PubMed:23896122). As a substrate of RNF185 interacting with SQSTM1, might also be involved in mitochondrial autophagy (Probable). {ECO:0000269|PubMed:15272311, ECO:0000269|PubMed:23896122, ECO:0000269|PubMed:7954800, ECO:0000305|PubMed:21931693}.;
Recessive Scores
- pRec
- 0.145
Intolerance Scores
- LoFtool
- 0.874
- RVIS EVS
- -0.12
- RVIS percentile EVS
- 45.13
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |