VAMP7
protein-codingvesicle associated membrane protein 7, the group of Pseudoautosomal region 2|Vesicle associated membrane proteins
Gene summary
This gene encodes a transmembrane protein that is a member of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) family. The encoded protein localizes to late endosomes and lysosomes and is involved in the fusion of transport vesicles to their target membranes. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Jun 2010]
- SYBL1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~62.4 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 VAMP7 variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . 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 | 2 | 2 | ||||
| missense | 6 | 2 | 8 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 0 | 6 | 4 | 10 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| Ensembl | ENSP00000286448.6 | 7 | MANE Select | |
| RefSeq | NP_001138621.1 | 12 | Standard | |
| RefSeq | NP_001172112.1 | 12 | Standard | |
| RefSeq | NP_005629.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- SNARE interactions in vesicular transport - Homo sapiens (human)
- Golgi Associated Vesicle Biogenesis
- Lysosome Vesicle Biogenesis
- Clathrin derived vesicle budding
- Interleukin-12 family signaling
Biological Process
- exocytosis
- endoplasmic reticulum to Golgi vesicle-mediated transport
- vesicle fusion
- phagocytosis, engulfment
- endosome to lysosome transport
Molecular Function
- SNARE binding
- SNAP receptor activity
- protein binding
- syntaxin binding
Cellular Component
- cytoplasm
- lysosomal membrane
- endoplasmic reticulum membrane
- trans-Golgi network
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262640
- Coding exons
- 6
- Length
- 62478
- Individuals with no LoFs
- 125577
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 125583
- p
- 0.0000239
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.656 | 115 | 137 | 0.842 | 0.00000659 | 1709 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000026 | 0.000026 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.0934
Intolerance Scores
- LoFtool
- 0.829
- RVIS EVS
- 0.15
- RVIS percentile EVS
- 64.32
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.353
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |