VDAC1
voltage dependent anion channel 1, the group of Voltage dependent anion channels
Basic information
Region (hg38): 5:133971871-134004975
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 VDAC1 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in VDAC1
This is a list of pathogenic ClinVar variants found in the VDAC1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-133973793-G-C | not specified | Uncertain significance (Sep 22, 2022) | ||
| 5-133975923-G-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 5-133975936-C-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 5-133980778-T-C | not specified | Uncertain significance (Aug 12, 2022) | ||
| 5-133980826-C-T | not specified | Uncertain significance (Mar 20, 2024) | ||
| 5-133980843-T-C | not specified | Uncertain significance (Dec 15, 2022) | ||
| 5-133980927-T-C | not specified | Uncertain significance (Nov 09, 2022) | ||
| 5-133991088-A-T | not specified | Uncertain significance (Sep 16, 2021) | ||
| 5-133991089-C-G | not specified | Uncertain significance (Feb 16, 2023) | ||
| 5-133991108-G-A | not specified | Uncertain significance (May 30, 2023) | ||
| 5-133992969-C-G | not specified | Uncertain significance (Nov 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VDAC1 | protein_coding | protein_coding | ENST00000265333 | 8 | 33219 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.973 | 0.0273 | 125732 | 0 | 1 | 125733 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.33 | 114 | 161 | 0.706 | 0.00000920 | 1827 |
| Missense in Polyphen | 27 | 33.432 | 0.80761 | 497 | ||
| Synonymous | 0.443 | 63 | 67.6 | 0.931 | 0.00000449 | 559 |
| Loss of Function | 3.41 | 1 | 15.5 | 0.0645 | 7.41e-7 | 187 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Forms a channel through the mitochondrial outer membrane and also the plasma membrane. The channel at the outer mitochondrial membrane allows diffusion of small hydrophilic molecules; in the plasma membrane it is involved in cell volume regulation and apoptosis. It adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The open state has a weak anion selectivity whereas the closed state is cation-selective (PubMed:11845315, PubMed:18755977, PubMed:20230784, PubMed:8420959). May participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis (PubMed:15033708, PubMed:25296756). {ECO:0000269|PubMed:11845315, ECO:0000269|PubMed:15033708, ECO:0000269|PubMed:18755977, ECO:0000269|PubMed:20230784, ECO:0000269|PubMed:25296756, ECO:0000269|PubMed:8420959}.;
- Pathway
- Benzodiazepine Pathway, Pharmacodynamics;Influenza A - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Necroptosis - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Cholesterol metabolism - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Transport of small molecules;Pink/Parkin Mediated Mitophagy;Mitophagy;Ub-specific processing proteases;Deubiquitination;Mitochondrial protein import;Mitochondrial calcium ion transport
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.3
- rvis_percentile_EVS
- 32.62
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.641
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.643
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vdac1
- Phenotype
- growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- pyruvate metabolic process;anion transport;apoptotic process;inorganic anion transport;viral process;macroautophagy;epithelial cell differentiation;anion transmembrane transport;regulation of autophagy of mitochondrion
- Cellular component
- nucleus;mitochondrion;mitochondrial outer membrane;mitochondrial permeability transition pore complex;plasma membrane;membrane;mitochondrial nucleoid;membrane raft;pore complex;extracellular exosome
- Molecular function
- protein binding;voltage-gated anion channel activity;porin activity;protein kinase binding;identical protein binding;ion channel binding