VAMP2
vesicle associated membrane protein 2, the group of Vesicle associated membrane proteins
Basic information
Region (hg38): 17:8159149-8163546
Previous symbols: [ "SYB2" ]
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements (Moderate), mode of inheritance: AD
- neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements (Strong), mode of inheritance: AD
- neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Neurodevelopmental disorder with hypotonia and autistic features with or without hyperkinetic movements | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 30929742 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (22 variants)
- Inborn_genetic_diseases (13 variants)
- Neurodevelopmental_disorder_with_hypotonia_and_autistic_features_with_or_without_hyperkinetic_movements (9 variants)
- VAMP2-related_disorder (5 variants)
- Neurodevelopmental_disorder (1 variants)
- Severe_neurodevelopmental_delay (1 variants)
- not_specified (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAMP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014232.3. 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 | 5 | |||||
| missense | 22 | 30 | ||||
| nonsense | 3 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 6 | 4 | 25 | 7 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VAMP2 | protein_coding | protein_coding | ENST00000316509 | 5 | 4398 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.887 | 0.112 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.41 | 36 | 69.0 | 0.521 | 0.00000377 | 752 |
| Missense in Polyphen | 1 | 16.956 | 0.058976 | 209 | ||
| Synonymous | -1.26 | 36 | 27.6 | 1.30 | 0.00000169 | 232 |
| Loss of Function | 2.47 | 0 | 7.10 | 0.00 | 3.87e-7 | 78 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| 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:
- Function
- FUNCTION: Involved in the targeting and/or fusion of transport vesicles to their target membrane. Modulates the gating characteristics of the delayed rectifier voltage-dependent potassium channel KCNB1. {ECO:0000250|UniProtKB:P63045}.;
- Pathway
- Synaptic vesicle cycle - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Salivary secretion - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Synaptic Vesicle Pathway;Insulin Signaling;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Disease;trans-Golgi Network Vesicle Budding;Other interleukin signaling;Signaling by Interleukins;Vesicle-mediated transport;Membrane Trafficking;Cytokine Signaling in Immune system;Toxicity of tetanus toxin (TeNT);Effects of Botulinum toxin;Toxicity of botulinum toxin type D (BoNT/D);Toxicity of botulinum toxin type F (BoNT/F);Uptake and actions of bacterial toxins;Toxicity of botulinum toxin type G (BoNT/G);Neurotoxicity of clostridium toxins;Infectious disease;Immune System;Neuronal System;Clathrin-mediated endocytosis;Glutamate Neurotransmitter Release Cycle;Dopamine Neurotransmitter Release Cycle;Acetylcholine Neurotransmitter Release Cycle;Toxicity of botulinum toxin type B (BoNT/B);GABA synthesis, release, reuptake and degradation;Neurotransmitter release cycle;Cargo recognition for clathrin-mediated endocytosis;Transmission across Chemical Synapses;Serotonin Neurotransmitter Release Cycle;Norepinephrine Neurotransmitter Release Cycle;Insulin-mediated glucose transport
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.425
- hipred
- Y
- hipred_score
- 0.598
- ghis
- 0.648
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Mouse Genome Informatics
- Gene name
- Vamp2
- Phenotype
- 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); normal 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); endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- exocytosis;response to glucose;glutamate secretion;protein transport;synaptic vesicle exocytosis;vesicle-mediated transport;calcium ion regulated exocytosis;regulation of exocytosis;cellular response to insulin stimulus;Golgi to plasma membrane protein transport;eosinophil degranulation;neutrophil degranulation;natural killer cell degranulation;long-term synaptic potentiation;regulation of vesicle-mediated transport;membrane organization;membrane fusion;protein-containing complex assembly;mucus secretion;positive regulation of intracellular protein transport;regulation of delayed rectifier potassium channel activity;regulation of histamine secretion by mast cell
- Cellular component
- trans-Golgi network;cytosol;plasma membrane;integral component of plasma membrane;synaptic vesicle;voltage-gated potassium channel complex;membrane;cell junction;clathrin-coated vesicle;secretory granule;clathrin-coated vesicle membrane;secretory granule membrane;synaptic vesicle membrane;SNARE complex;cytoplasmic vesicle;vesicle;zymogen granule membrane;neuron projection;intracellular membrane-bounded organelle;neuron projection terminus;synapse;perinuclear region of cytoplasm;clathrin-sculpted glutamate transport vesicle membrane;clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane;synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex;synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex;synaptobrevin 2-SNAP-25-syntaxin-1a complex;clathrin-sculpted monoamine transport vesicle membrane
- Molecular function
- SNARE binding;protein binding;calmodulin binding;phospholipid binding;syntaxin-1 binding;syntaxin binding;protein self-association;calcium-dependent protein binding