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VDAC3 voltage dependent anion channel 3 [ Homo sapiens (human) ]

Gene ID: 7419, updated on 27-Nov-2024

Summary

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Official Symbol
VDAC3provided by HGNC
Official Full Name
voltage dependent anion channel 3provided by HGNC
Primary source
HGNC:HGNC:12674
See related
Ensembl:ENSG00000078668 MIM:610029; AllianceGenome:HGNC:12674
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
VDAC-3; HD-VDAC3
Summary
This gene encodes a voltage-dependent anion channel (VDAC), and belongs to the mitochondrial porin family. VDACs are small, integral membrane proteins that traverse the outer mitochondrial membrane and conduct ATP and other small metabolites. They are known to bind several kinases of intermediary metabolism, thought to be involved in translocation of adenine nucleotides, and are hypothesized to form part of the mitochondrial permeability transition pore, which results in the release of cytochrome c at the onset of apoptotic cell death. Alternatively transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Oct 2011]
Expression
Ubiquitous expression in heart (RPKM 97.4), testis (RPKM 53.6) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See VDAC3 in Genome Data Viewer
Location:
8p11.21
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (42391880..42405937)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (42662194..42676251)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (42249398..42263455)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L5 pseudogene 23 Neighboring gene DNA polymerase beta Neighboring gene H3K27ac hESC enhancers GRCh37_chr8:42248902-42249402 and GRCh37_chr8:42249403-42249903 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:42258699-42258918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27311 Neighboring gene dickkopf WNT signaling pathway inhibitor 4 Neighboring gene solute carrier family 20 member 2 Neighboring gene Sharpr-MPRA regulatory region 15103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:42331955-42332466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:42332467-42332978 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:42333977-42334500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:42333451-42333976 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:42350219-42351086 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:42359656-42360855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19157 Neighboring gene Sharpr-MPRA regulatory region 9023 Neighboring gene NANOG hESC enhancer GRCh37_chr8:42409514-42410035 Neighboring gene small integral membrane protein 19 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27312 Neighboring gene Sharpr-MPRA regulatory region 2659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:42516917-42517417 Neighboring gene uncharacterized LOC124900250 Neighboring gene cholinergic receptor nicotinic beta 3 subunit

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Isolation of a novel human voltage-dependent anion channel gene. Rahmani Z, et al. Eur J Hum Genet, 1998 Jul-Aug. PMID 9781040
  2. Association of the VDAC3 gene polymorphism with sperm count in Han-Chinese population with idiopathic male infertility. Pan L, et al. Oncotarget, 2017 Jul 11. PMID 28431403, Free PMC Article
  3. The tissue-specific, alternatively spliced single ATG exon of the type 3 voltage-dependent anion channel gene does not create a truncated protein isoform in vivo. Decker WK, et al. Mol Genet Metab, 2000 May. PMID 10833333
  4. VDAC3 gating is activated by suppression of disulfide-bond formation between the N-terminal region and the bottom of the pore. Okazaki M, et al. Biochim Biophys Acta, 2015 Dec. PMID 26407725
  5. A computational study of ion current modulation in hVDAC3 induced by disulfide bonds. Guardiani C, et al. Biochim Biophys Acta, 2016 Apr. PMID 26806159

See all (148) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Specific Post-Translational Modifications of VDAC3 in ALS-SOD1 Model Cells Identified by High-Resolution Mass Spectrometry.
    Title: Specific Post-Translational Modifications of VDAC3 in ALS-SOD1 Model Cells Identified by High-Resolution Mass Spectrometry.
  2. A lower affinity to cytosolic proteins reveals VDAC3 isoform-specific role in mitochondrial biology.
    Title: A lower affinity to cytosolic proteins reveals VDAC3 isoform-specific role in mitochondrial biology.
  3. A High Resolution Mass Spectrometry Study Reveals the Potential of Disulfide Formation in Human Mitochondrial Voltage-Dependent Anion Selective Channel Isoforms (hVDACs).
    Title: A High Resolution Mass Spectrometry Study Reveals the Potential of Disulfide Formation in Human Mitochondrial Voltage-Dependent Anion Selective Channel Isoforms (hVDACs).
  4. Expression of voltage-dependent anion channels in endometrial cancer and its potential prognostic significance.
    Title: Expression of voltage-dependent anion channels in endometrial cancer and its potential prognostic significance.
  5. VDAC3 role in the melanoma drug resistance to erastin.Erastin-induced resistance mediated by FOXM1-Nedd4-VDAC2/VDAC3 negative feedback loop in melanoma.Nedd4 ubiquitinates and degrades VDAC3.
    Title: Nedd4 ubiquitylates VDAC2/3 to suppress erastin-induced ferroptosis in melanoma.
  6. Data suggest that the hub genes NADH:ubiquinone oxidoreductase subunit B5 (NDUFB5), translocase of inner mitochondrial membrane domain containing 1 (TIMMDC1), and voltage-dependent anion channel 3 (VDAC3) might serve as potential biomarkers for diagnosis and/or therapeutic targets for precise treatment of septic cardiomyopathy (SC) .
    Title: Potentially Critical Roles of NDUFB5, TIMMDC1, and VDAC3 in the Progression of Septic Cardiomyopathy Through Integrated Bioinformatics Analysis.
  7. The AG genotype of rs16891278 showed a significantly lower sperm concentration compared with the AA genotype (P = 0.044). Findings suggest that VDAC3 genetic variants may be associated with human sperm count.
    Title: Association of the VDAC3 gene polymorphism with sperm count in Han-Chinese population with idiopathic male infertility.
  8. This cohort study showed that the VDAC3 gene was down regulation between patients with idiopathic Parkinson disease and controls
    Title: Analysis of blood-based gene expression in idiopathic Parkinson disease.
  9. The works available on VDAC cysteines support the notion that VDAC1, VDAC2, and VDAC3 proteins are paralogs with a similar pore-function and slightly different, but important, ancillary biological functions. (Review)
    Title: Role of cysteines in mammalian VDAC isoforms' function.
  10. VDAC3 is able to modulate its pore size and current by exploiting the mobility of the N-terminal and forming, upon external stimuli, disulfide bridges with cysteine residues located on the barrel and exposed to the inter-membrane space.
    Title: A computational study of ion current modulation in hVDAC3 induced by disulfide bonds.
Submit: New GeneRIF Correction See all GeneRIFs (21)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 is identified to have a physical interaction with voltage-dependent anion channel 3 (VDAC3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
Vpr vpr The G5 domain of gelsolin inhibits HIV-Vpr-induced T-cell apoptosis by blocking the interaction between Vpr and VDAC PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables porin activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables voltage-gated monoatomic anion channel activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables voltage-gated monoatomic anion channel activity TAS
Traceable Author Statement
more info
 PubMed 
enables voltage-gated monoatomic ion channel activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in adenine transport TAS
Traceable Author Statement
more info
 PubMed 
involved_in behavioral fear response IEA
Inferred from Electronic Annotation
more info
  
involved_in learning IEA
Inferred from Electronic Annotation
more info
  
involved_in monoatomic anion transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in neuron-neuron synaptic transmission IEA
Inferred from Electronic Annotation
more info
  
involved_in sperm mitochondrial sheath assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in mitochondrial outer membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrial outer membrane TAS
Traceable Author Statement
more info
  
located_in mitochondrion HDA PubMed 
located_in mitochondrion HTP PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
located_in nucleus HDA PubMed 
part_of pore complex IEA
Inferred from Electronic Annotation
more info
  
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
voltage-dependent anion-selective channel protein 3
Names
outer mitochondrial membrane protein porin 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001135694.3 → NP_001129166.1  voltage-dependent anion-selective channel protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001129166.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an additional, in-frame 3 nt coding exon compared to variant 1. This results in an isoform (2) that is 1 aa longer than isoform 1. The short exon is supported by PMID:10833333, and orthologs in mouse, rat and bovine.
    Source sequence(s)
    AC107885
    Consensus CDS
    CCDS47850.1
    UniProtKB/Swiss-Prot
    Q9Y277
    Related
    ENSP00000428845.1, ENST00000521158.5
    Conserved Domains (1) summary
    cd07306
    Location:5 → 283
    Porin3_VDAC; Voltage-dependent anion channel of the outer mitochondrial membrane

  2. NM_001413552.1 → NP_001400481.1  voltage-dependent anion-selective channel protein 3 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC107885
    UniProtKB/Swiss-Prot
    Q9UIS0, Q9Y277

  3. NM_001413553.1 → NP_001400482.1  voltage-dependent anion-selective channel protein 3 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC107885

  4. NM_001413554.1 → NP_001400483.1  voltage-dependent anion-selective channel protein 3 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC107885

  5. NM_001413555.1 → NP_001400484.1  voltage-dependent anion-selective channel protein 3 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC107885

  6. NM_001413556.1 → NP_001400485.1  voltage-dependent anion-selective channel protein 3 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC107885

  7. NM_001413557.1 → NP_001400486.1  voltage-dependent anion-selective channel protein 3 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC107885

  8. NM_001413558.1 → NP_001400487.1  voltage-dependent anion-selective channel protein 3 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC107885
    UniProtKB/Swiss-Prot
    Q9UIS0, Q9Y277

  9. NM_001413559.1 → NP_001400488.1  voltage-dependent anion-selective channel protein 3 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC107885

  10. NM_001413560.1 → NP_001400489.1  voltage-dependent anion-selective channel protein 3 isoform 9

    Status: REVIEWED

    Source sequence(s)
    AC107885

  11. NM_001413561.1 → NP_001400490.1  voltage-dependent anion-selective channel protein 3 isoform 10

    Status: REVIEWED

    Source sequence(s)
    AC107885

  12. NM_005662.7 → NP_005653.3  voltage-dependent anion-selective channel protein 3 isoform 1

    See identical proteins and their annotated locations for NP_005653.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript, and encodes isoform 1.
    Source sequence(s)
    BC056870, BQ001504, DA930673
    Consensus CDS
    CCDS6131.1
    UniProtKB/Swiss-Prot
    Q9UIS0, Q9Y277
    Related
    ENSP00000022615.4, ENST00000022615.9
    Conserved Domains (1) summary
    cd07306
    Location:5 → 282
    Porin3_VDAC; Voltage-dependent anion channel of the outer mitochondrial membrane

RNA

  1. NR_182160.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC107885

  2. NR_182161.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC107885

  3. NR_182162.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC107885

  4. NR_182163.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC107885

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    42391880..42405937
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    42662194..42676251
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y277.1 GenPept UniProtKB/Swiss-Prot:Q9Y277

Gene LinkOut

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