VAMP7
vesicle associated membrane protein 7, the group of Pseudoautosomal region 2|Vesicle associated membrane proteins
Basic information
Region (hg38): Y:57067865-57130289
Previous symbols: [ "SYBL1" ]
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 VAMP7 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 0 | 6 | 4 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VAMP7 | protein_coding | protein_coding | ENST00000262640 | 6 | 62478 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0138 | 0.959 | 125577 | 0 | 6 | 125583 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.656 | 115 | 137 | 0.842 | 0.00000659 | 1709 |
| Missense in Polyphen | 33 | 39.12 | 0.84355 | 484 | ||
| Synonymous | 0.158 | 48 | 49.4 | 0.971 | 0.00000254 | 468 |
| Loss of Function | 1.92 | 5 | 12.3 | 0.408 | 6.02e-7 | 144 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the targeting and/or fusion of transport vesicles to their target membrane during transport of proteins from the early endosome to the lysosome. Required for heterotypic fusion of late endosomes with lysosomes and homotypic lysosomal fusion. Required for calcium regulated lysosomal exocytosis. Involved in the export of chylomicrons from the endoplasmic reticulum to the cis Golgi. Required for exocytosis of mediators during eosinophil and neutrophil degranulation, and target cell killing by natural killer cells. Required for focal exocytosis of late endocytic vesicles during phagosome formation. {ECO:0000269|PubMed:10888671, ECO:0000269|PubMed:16677249, ECO:0000269|PubMed:18042464}.;
- Pathway
- SNARE interactions in vesicular transport - Homo sapiens (human);Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Interleukin-12 family signaling;trans-Golgi Network Vesicle Budding;Signaling by Interleukins;Vesicle-mediated transport;Membrane Trafficking;Cytokine Signaling in Immune system;Immune System;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;Interleukin-12 signaling
(Consensus)
Recessive Scores
- pRec
- 0.0934
Intolerance Scores
- loftool
- 0.829
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.32
Haploinsufficiency Scores
- pHI
- 0.221
- hipred
- N
- hipred_score
- 0.292
- ghis
- 0.564
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.353
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vamp7
- 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); homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- exocytosis;endoplasmic reticulum to Golgi vesicle-mediated transport;vesicle fusion;phagocytosis, engulfment;endosome to lysosome transport;vesicle-mediated transport;calcium ion regulated exocytosis;triglyceride transport;SNARE complex assembly;Golgi to plasma membrane protein transport;eosinophil degranulation;neutrophil degranulation;natural killer cell degranulation;vesicle transport along microtubule;vesicle fusion with Golgi apparatus;positive regulation of dendrite morphogenesis;membrane organization;autophagosome maturation;regulation of protein targeting to vacuolar membrane;positive regulation of histamine secretion by mast cell
- Cellular component
- cytoplasm;lysosomal membrane;endoplasmic reticulum membrane;trans-Golgi network;plasma membrane;cell surface;membrane;lamellipodium;cell junction;secretory granule;integral component of synaptic vesicle membrane;clathrin-coated vesicle membrane;secretory granule membrane;phagocytic vesicle membrane;platelet alpha granule;pseudopodium;SNARE complex;late endosome membrane;azurophil granule membrane;neuron projection;intracellular membrane-bounded organelle;apical part of cell;phagocytic vesicle;perinuclear region of cytoplasm;extracellular exosome;hippocampal mossy fiber to CA3 synapse
- Molecular function
- SNARE binding;SNAP receptor activity;protein binding;syntaxin binding