VAMP8
vesicle associated membrane protein 8, the group of Vesicle associated membrane proteins
Basic information
Region (hg38): 2:85561562-85582031
Links
Phenotypes
GenCC
Source:
No genCC data.
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 VAMP8 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 | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 6 | 0 | 1 |
Variants in VAMP8
This is a list of pathogenic ClinVar variants found in the VAMP8 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-85561615-C-A | Benign (Jul 09, 2018) | |||
| 2-85579034-A-G | not specified | Uncertain significance (Oct 19, 2024) | ||
| 2-85579040-G-C | not specified | Uncertain significance (Dec 09, 2023) | ||
| 2-85579121-A-G | not specified | Uncertain significance (Nov 15, 2023) | ||
| 2-85579124-A-T | not specified | Uncertain significance (Jul 31, 2023) | ||
| 2-85579138-C-T | not specified | Uncertain significance (Nov 10, 2022) | ||
| 2-85581638-G-C | not specified | Uncertain significance (Apr 19, 2024) | ||
| 2-85581684-A-G | not specified | Uncertain significance (Apr 25, 2022) | ||
| 2-85581859-T-C | Benign (Nov 02, 2020) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VAMP8 | protein_coding | protein_coding | ENST00000263864 | 3 | 20470 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.107 | 0.786 | 125740 | 0 | 8 | 125748 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.849 | 39 | 57.1 | 0.684 | 0.00000335 | 647 |
| Missense in Polyphen | 12 | 17.874 | 0.67136 | 230 | ||
| Synonymous | -0.535 | 24 | 20.9 | 1.15 | 0.00000123 | 189 |
| Loss of Function | 1.26 | 2 | 5.05 | 0.396 | 2.80e-7 | 54 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000577 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000278 | 0.0000264 |
| Middle Eastern | 0.0000577 | 0.0000544 |
| South Asian | 0.0000669 | 0.0000653 |
| Other | 0.000169 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: SNAREs, soluble N-ethylmaleimide-sensitive factor- attachment protein receptors, are essential proteins for fusion of cellular membranes. SNAREs localized on opposing membranes assemble to form a trans-SNARE complex, an extended, parallel four alpha-helical bundle that drives membrane fusion. VAMP8 is a SNARE involved in autophagy through the direct control of autophagosome membrane fusion with the lysososome membrane via its interaction with the STX17-SNAP29 binary t-SNARE complex (PubMed:23217709, PubMed:25686604). Also required for dense-granule secretion in platelets (PubMed:12130530). Plays also a role in regulated enzyme secretion in pancreatic acinar cells (By similarity). Involved in the abscission of the midbody during cell division, which leads to completely separate daughter cells (By similarity). Involved in the homotypic fusion of early and late endosomes (By similarity). {ECO:0000250|UniProtKB:Q9WUF4, ECO:0000269|PubMed:12130530, ECO:0000269|PubMed:23217709, ECO:0000269|PubMed:25686604}.;
- Pathway
- Platelet activation - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Neutrophil degranulation;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Innate Immune System;Immune System;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis
(Consensus)
Recessive Scores
- pRec
- 0.240
Intolerance Scores
- loftool
- 0.656
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.11
Haploinsufficiency Scores
- pHI
- 0.285
- hipred
- Y
- hipred_score
- 0.621
- ghis
- 0.443
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.945
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vamp8
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; 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); digestive/alimentary phenotype; renal/urinary system phenotype;
Gene ontology
- Biological process
- antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;protein transport;autophagosome membrane docking;eosinophil degranulation;neutrophil degranulation;viral entry into host cell;membrane organization;mucus secretion;autophagosome maturation;regulation of protein localization to plasma membrane;negative regulation of secretion by cell;positive regulation of histamine secretion by mast cell
- Cellular component
- cytoplasm;lysosomal membrane;early endosome;cytosol;plasma membrane;membrane;integral component of membrane;clathrin-coated vesicle membrane;secretory granule membrane;phagocytic vesicle membrane;SNARE complex;early endosome membrane;late endosome membrane;vesicle;azurophil granule membrane;specific granule membrane;perinuclear region of cytoplasm;recycling endosome;recycling endosome membrane;extracellular exosome;tertiary granule membrane;mucin granule
- Molecular function
- protein binding;chloride channel inhibitor activity