SNAP47
protein-codingsynaptosome associated protein 47
Gene summary
Predicted to enable SNAP receptor activity. Predicted to be involved in synaptic vesicle fusion to presynaptic active zone membrane and synaptic vesicle priming. Predicted to act upstream of or within long-term synaptic potentiation. Located in BLOC-1 complex. [provided by Alliance of Genome Resources, Jun 2026]
- C1orf142
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~53.6 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 SNAP47 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_053052.4. 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 | 4 | 4 | ||||
| missense | 57 | 7 | 64 | |||
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 67 | 7 | 0 | 74 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_444280.3 | 4 | MANE Select | |
| Ensembl | ENSP00000483253.1 | 4 | MANE Select | |
| RefSeq | NP_001310859.1 | 4 | Standard | |
| RefSeq | NP_001310860.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- exocytosis
- vesicle fusion
- synaptic vesicle priming
- synaptic vesicle fusion to presynaptic active zone membrane
- long-term synaptic potentiation
Molecular Function
- SNAP receptor activity
- protein binding
- syntaxin binding
Cellular Component
- plasma membrane
- dendrite
- synaptic vesicle membrane
- BLOC-1 complex
- SNARE complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000366759
- Coding exons
- 5
- Length
- 52688
- Individuals with no LoFs
- 125719
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 29
- Defined
- 125748
- p
- 0.000115
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.130 | 274 | 268 | 1.02 | 0.0000149 | 3001 |
| Missense (PolyPhen) | 64 | 81.239 | 0.7878 | 1017 | ||
| Synonymous | 0.691 | 103 | 112 | 0.917 | 0.00000690 | 954 |
| Loss of Function | 1.58 | 10 | 17.1 | 0.586 | 8.77e-7 | 189 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00060 | 0.00060 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in intracellular membrane fusion. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0974
Intolerance Scores
- LoFtool
- 0.604
- RVIS EVS
- 0.76
- RVIS percentile EVS
- 86.75
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.190
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |