VDAC2

voltage dependent anion channel 2, the group of Voltage dependent anion channels

Basic information

Region (hg38): 10:75210154-75231448

Links

ENSG00000165637 ∙ NCBI:7417 ∙ OMIM:193245 ∙ HGNC:12672 ∙ Uniprot:P45880 ∙ 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 VDAC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VDAC2 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					1	1
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	1

Variants in VDAC2

This is a list of pathogenic ClinVar variants found in the VDAC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-75214026-G-A		not specified	Uncertain significance (Sep 14, 2022)
10-75214054-A-G		not specified	Uncertain significance (Jun 06, 2023)
10-75214061-C-G		not specified	Uncertain significance (May 03, 2023)
10-75219150-C-G		not specified	Uncertain significance (Oct 05, 2023)
10-75219160-C-T		not specified	Uncertain significance (Aug 04, 2023)
10-75219332-A-T		not specified	Uncertain significance (Aug 04, 2021)
10-75220882-A-C		not specified	Uncertain significance (Dec 20, 2023)
10-75220903-T-G		not specified	Uncertain significance (Jun 16, 2024)
10-75220964-C-T		not specified	Uncertain significance (Jul 14, 2021)
10-75222254-A-G		Severe combined immunodeficiency disease	Uncertain significance (Mar 23, 2023)
10-75222255-T-C			Benign (Jun 21, 2018)
10-75230900-G-A		not specified	Uncertain significance (Jan 24, 2024)
10-75230912-C-T		not specified	Uncertain significance (Sep 26, 2023)
10-75230939-A-G		not specified	Uncertain significance (Mar 01, 2023)
10-75230945-G-A		not specified	Uncertain significance (Aug 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VDAC2	protein_coding	protein_coding	ENST00000313132	9	21295

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.634	0.366	125627	0	3	125630	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	118	159	0.744	0.00000736	2011
Missense in Polyphen		13	21.52	0.60409		308
Synonymous	-0.541	64	58.7	1.09	0.00000293	592
Loss of Function	3.05	3	16.3	0.185	6.88e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
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. The channel 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.
• 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);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: 0.158

Intolerance Scores

• loftool: 0.426
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.717
• hipred: Y
• hipred_score: 0.748
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.867

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vdac2
• Phenotype: immune system phenotype; hematopoietic system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: anion transport;binding of sperm to zona pellucida;inorganic anion transport;negative regulation of protein polymerization;anion transmembrane transport;negative regulation of intrinsic apoptotic signaling pathway
• Cellular component: acrosomal vesicle;nucleus;mitochondrion;mitochondrial outer membrane;synaptic vesicle;mitochondrial nucleoid;myelin sheath;pore complex
• Molecular function: nucleotide binding;protein binding;voltage-gated anion channel activity;porin activity