SNAPC1
protein-codingsmall nuclear RNA activating complex polypeptide 1, the group of SNAP complex
Gene summary
Predicted to enable sequence-specific DNA binding activity. Predicted to be involved in snRNA transcription by RNA polymerase II and snRNA transcription by RNA polymerase III. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~34.0 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 SNAPC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003082.4. 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 | 1 | 1 | ||||
| missense | 47 | 47 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 49 | 0 | 0 | 49 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003073.1 | 10 | MANE Select | |
| Ensembl | ENSP00000216294.4 | 10 | MANE Select | |
| Ensembl | ENSP00000593692.1 | 9 | Standard | |
| Ensembl | ENSP00000593692.1 | 9 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| snapc1b | Danio rerio | Structure: macrophage Quality: increased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Gene expression (Transcription)
- RNA polymerase II transcribes snRNA genes
- RNA Polymerase II Transcription
- RNA Polymerase III Abortive And Retractive Initiation
- RNA Polymerase III Transcription Initiation From Type 3 Promoter
Biological Process
- snRNA transcription by RNA polymerase II
- snRNA transcription by RNA polymerase III
Molecular Function
- sequence-specific DNA binding
Cellular Component
- nucleus
- nucleoplasm
- nucleolus
- snRNA-activating protein complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000216294
- Coding exons
- 10
- Length
- 34072
- Individuals with no LoFs
- 124906
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 839
- Defined
- 125747
- p
- 0.00335
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.000465 | 180 | 180 | 1.00 | 0.00000838 | 2435 |
| Missense (PolyPhen) | 35 | 41.218 | 0.84914 | 583 | ||
| Synonymous | -0.650 | 69 | 62.5 | 1.10 | 0.00000287 | 625 |
| Loss of Function | -0.338 | 23 | 21.3 | 1.08 | 0.00000116 | 274 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0016 | 0.0016 | notable |
| Latino/Admixed American | 0.0016 | 0.0015 | notable |
| Ashkenazi Jewish | 0.00011 | 0.000099 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.0035 | 0.0035 | notable |
| European (Non-Finnish) | 0.0055 | 0.0054 | notable |
| South Asian | 0.0014 | 0.0014 | notable |
| Other | 0.0047 | 0.0046 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. Binds to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Recruits TBP and BRF2 to the U6 snRNA TATA box. {ECO:0000269|PubMed:12621023}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- LoFtool
- 0.429
- RVIS EVS
- 0
- RVIS percentile EVS
- 53.73
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.887
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |