VAMP4
Basic information
Region (hg38): 1:171700160-171742074
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAMP4 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in VAMP4
This is a list of pathogenic ClinVar variants found in the VAMP4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-171704528-A-G | not specified | Uncertain significance (Aug 08, 2023) | ||
| 1-171704529-T-C | not specified | Uncertain significance (Jan 16, 2024) | ||
| 1-171706406-T-C | not specified | Uncertain significance (Dec 01, 2022) | ||
| 1-171709706-A-C | not specified | Uncertain significance (Aug 12, 2021) | ||
| 1-171738372-T-A | not specified | Uncertain significance (Dec 18, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VAMP4 | protein_coding | protein_coding | ENST00000236192 | 7 | 42088 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.144 | 0.839 | 125741 | 0 | 4 | 125745 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.680 | 57 | 73.4 | 0.777 | 0.00000367 | 936 |
| Missense in Polyphen | 9 | 14.977 | 0.60091 | 237 | ||
| Synonymous | 1.42 | 14 | 22.6 | 0.619 | 0.00000105 | 239 |
| Loss of Function | 2.06 | 3 | 10.1 | 0.298 | 4.91e-7 | 124 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000905 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000881 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000339 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the pathway that functions to remove an inhibitor (probably synaptotagmin-4) of calcium-triggered exocytosis during the maturation of secretory granules. May be a marker for this sorting pathway that is critical for remodeling the secretory response of granule.;
- Pathway
- SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Recessive Scores
- pRec
- 0.124
Intolerance Scores
- loftool
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.767
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.648
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.970
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vamp4
- Phenotype
Gene ontology
- Biological process
- microtubule cytoskeleton organization;endoplasmic reticulum to Golgi vesicle-mediated transport;synaptic vesicle to endosome fusion;SNARE complex assembly;Golgi to plasma membrane protein transport;membrane organization;Golgi ribbon formation;regulation of synaptic vesicle endocytosis
- Cellular component
- Golgi membrane;lysosome;endosome;Golgi apparatus;plasma membrane;cell surface;transport vesicle;integral component of synaptic vesicle membrane;clathrin-coated vesicle membrane;trans-Golgi network membrane
- Molecular function
- protein binding