VDAC3

voltage dependent anion channel 3, the group of Voltage dependent anion channels

Basic information

Region (hg38): 8:42391624-42405937

Links

ENSG00000078668 ∙ NCBI:7419 ∙ OMIM:610029 ∙ HGNC:12674 ∙ Uniprot:Q9Y277 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VDAC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VDAC3 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in VDAC3

This is a list of pathogenic ClinVar variants found in the VDAC3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-42394269-A-C		not specified	Uncertain significance (May 30, 2024)
8-42395122-T-G		not specified	Uncertain significance (Dec 13, 2022)
8-42398725-C-T		not specified	Uncertain significance (Mar 15, 2024)
8-42398740-C-T		not specified	Uncertain significance (May 26, 2022)
8-42398746-C-G		not specified	Uncertain significance (Aug 13, 2021)
8-42398826-G-T		not specified	Uncertain significance (Jan 04, 2024)
8-42401883-G-C		not specified	Uncertain significance (Dec 09, 2023)
8-42401903-G-A		not specified	Uncertain significance (Nov 01, 2022)
8-42403358-A-G		not specified	Uncertain significance (Aug 10, 2021)
8-42403393-G-A		not specified	Uncertain significance (May 17, 2023)
8-42403412-G-A		not specified	Uncertain significance (Feb 14, 2023)
8-42405443-G-A		not specified	Uncertain significance (Jun 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VDAC3	protein_coding	protein_coding	ENST00000521158	9	14274

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00546	125740	0	4	125744	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	113	151	0.749	0.00000739	1860
Missense in Polyphen		23	44.778	0.51365		629
Synonymous	1.89	39	57.2	0.682	0.00000302	536
Loss of Function	3.64	0	15.5	0.00	7.15e-7	202

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)	0.0000264	0.0000264
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 that allows diffusion of small hydrophilic molecules. {ECO:0000250}.
• Pathway: 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);Viral carcinogenesis - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Ferroptosis - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Transport of small molecules;Ub-specific processing proteases;Deubiquitination;Mitochondrial calcium ion transport (Consensus)

Recessive Scores

• pRec: 0.0897

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.665
• hipred: N
• hipred_score: 0.401
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Vdac3
• Phenotype: cellular phenotype; muscle phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; 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); 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); reproductive system phenotype

Gene ontology

• Biological process: behavioral fear response;neuron-neuron synaptic transmission;learning;inorganic anion transport;adenine transport;anion transmembrane transport;regulation of cilium assembly
• Cellular component: nucleus;mitochondrion;mitochondrial outer membrane;pore complex;extracellular exosome
• Molecular function: nucleotide binding;voltage-gated anion channel activity;porin activity