VDAC1

voltage dependent anion channel 1, the group of Voltage dependent anion channels

Basic information

Region (hg38): 5:133971871-134004975

Links

ENSG00000213585 ∙ NCBI:7416 ∙ OMIM:604492 ∙ HGNC:12669 ∙ Uniprot:P21796 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 70.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000265333.8	ENSP00000265333.3	8	yes	-
ENST00000395044.7	ENSP00000378484.3	8	-	-
ENST00000395047.6	ENSP00000378487.2	8	-	-
ENST00000425992.2	ENSP00000390129.1	5	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VDAC1 gene.

• not_specified (24 variants)

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. These statistics are base on transcript: NM_000003374.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			25			25
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)			4			4
Total	0	0	30	0	0

GnomAD

Source: gnomAD

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
		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: dbNSFP

• 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

• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

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

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