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.

not_specified (27 variants)

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. These statistics are base on transcript: NM_000005662.7. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			27 clinvar			27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	0	0

Loading clinvar variants...

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

loftool
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