VGF
protein-codingVGF nerve growth factor inducible, the group of Granins
Gene summary
This gene is specifically expressed in a subpopulation of neuroendocrine cells, and is upregulated by nerve growth factor. The structural organization of this gene is similar to that of the rat gene, and both the translated and the untranslated regions show a high degree of sequence similarity to the rat gene. The encoded secretory protein also shares similarities with the secretogranin/chromogranin family, however, its exact function is not known. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to VGF variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003378.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 5 | 3 | 8 | |||
| missense | 111 | 1 | 1 | 113 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 111 | 6 | 4 | 121 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003369.2 | 1 | MANE Select | |
| Ensembl | ENSP00000249330.2 | 1 | MANE Select | |
| Ensembl | ENSP00000400884.2 | 1 | Standard | |
| Ensembl | ENSP00000400884.2 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- ovarian follicle development
- response to dietary excess
- generation of precursor metabolites and energy
- response to cold
- regulation of signaling receptor activity
Molecular Function
- molecular_function
- neuropeptide hormone activity
- growth factor activity
Cellular Component
- extracellular space
- endoplasmic reticulum lumen
- Golgi apparatus
- transport vesicle
- cytoplasmic vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000249330
- Coding exons
- 1
- Length
- 3085
- Individuals with no LoFs
- 121942
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 121944
- p
- 0.00000820
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.251 | 316 | 329 | 0.961 | 0.0000152 | 3814 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00016 | 0.00013 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.194
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.417
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |