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

    Gene ID: 7419, updated on 7-Apr-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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    Location:
    8p11.21
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (42391880..42405937)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (42662194..42676251)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (42249279..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. Specific Post-Translational Modifications of VDAC3 in ALS-SOD1 Model Cells Identified by High-Resolution Mass Spectrometry. Pittalà MGG, et al. Int J Mol Sci, 2022 Dec 13. PMID 36555496, Free PMC Article
    2. A lower affinity to cytosolic proteins reveals VDAC3 isoform-specific role in mitochondrial biology. Queralt-Martín M, et al. J Gen Physiol, 2020 Feb 3. PMID 31935282, Free PMC Article
    3. 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
    4. A computational study of ion current modulation in hVDAC3 induced by disulfide bonds. Guardiani C, et al. Biochim Biophys Acta, 2016 Apr. PMID 26806159
    5. 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

    See all (122) 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)

    Genotypes

    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 
    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 mitochondrion HDA 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_2023_10

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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