VGF

VGF nerve growth factor inducible, the group of Granins

Basic information

Region (hg38): 7:101162509-101165569

Links

ENSG00000128564 ∙ NCBI:7425 ∙ OMIM:602186 ∙ HGNC:12684 ∙ Uniprot:O15240 ∙ 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 VGF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VGF 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				4	3	7
missense			49	1	1	51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	5	4

Variants in VGF

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

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

Position	Type	Phenotype	Significance	ClinVar
7-101163121-G-A		not specified	Uncertain significance (Aug 17, 2022)
7-101163150-T-C		not specified	Uncertain significance (Sep 14, 2022)
7-101163186-C-T		not specified	Uncertain significance (Nov 08, 2022)
7-101163201-T-C		not specified	Uncertain significance (Oct 07, 2022)
7-101163242-C-G		not specified	Uncertain significance (Jul 12, 2023)
7-101163253-C-A		not specified	Uncertain significance (Jul 14, 2023)
7-101163280-C-A		not specified	Uncertain significance (Jul 25, 2023)
7-101163289-C-T		not specified	Uncertain significance (Sep 26, 2023)
7-101163294-C-A		not specified	Uncertain significance (Jun 21, 2022)
7-101163309-G-A		not specified	Uncertain significance (Dec 28, 2023)
7-101163318-G-A		not specified	Uncertain significance (Dec 07, 2023)
7-101163321-G-A		not specified	Uncertain significance (Sep 16, 2021)
7-101163336-A-G		not specified	Uncertain significance (Jan 03, 2024)
7-101163358-C-A		not specified	Uncertain significance (Mar 07, 2024)
7-101163363-G-T		not specified	Uncertain significance (Jun 02, 2023)
7-101163366-G-C		not specified	Uncertain significance (May 31, 2024)
7-101163366-G-T		not specified	Uncertain significance (Aug 01, 2023)
7-101163368-C-G			Benign/Likely benign (May 01, 2022)
7-101163376-G-A		not specified	Uncertain significance (Mar 01, 2024)
7-101163518-C-G		not specified	Likely benign (Jan 04, 2022)
7-101163542-C-G			Likely benign (Nov 14, 2018)
7-101163558-C-T		not specified	Uncertain significance (Jan 05, 2022)
7-101163561-C-G		not specified	Uncertain significance (Jul 20, 2022)
7-101163561-C-T		not specified	Uncertain significance (Feb 23, 2023)
7-101163565-G-A		not specified	Uncertain significance (Mar 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VGF	protein_coding	protein_coding	ENST00000249330	1	3085

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.568	0.431	121942	0	2	121944	0.00000820

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.251	316	329	0.961	0.0000152	3814
Missense in Polyphen		94	102.33	0.91862		1212
Synonymous	-1.27	174	154	1.13	0.00000759	1345
Loss of Function	2.94	3	15.5	0.193	6.83e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000156	0.000126
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the regulation of cell-cell interactions or in synatogenesis during the maturation of the nervous system. {ECO:0000250}.; FUNCTION: Antimicrobial peptide VGF[554-577]: Has bactericidal activity against M. luteus, and antifungal activity against P. Pastoris. {ECO:0000269|PubMed:23250050}.
• Pathway: Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.194

Haploinsufficiency Scores

• pHI: 0.380
• hipred: Y
• hipred_score: 0.622
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.417

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vgf
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: ovarian follicle development;response to dietary excess;generation of precursor metabolites and energy;response to cold;regulation of signaling receptor activity;sexual reproduction;insulin secretion;response to insulin;glucose homeostasis;defense response to bacterium;post-translational protein modification;cellular protein metabolic process;response to cAMP
• Cellular component: extracellular space;endoplasmic reticulum lumen;Golgi apparatus;transport vesicle;cytoplasmic vesicle;intracellular membrane-bounded organelle
• Molecular function: molecular_function;neuropeptide hormone activity;growth factor activity