SPATC1
protein-codingspermatogenesis and centriole associated 1
Gene summary
Predicted to enable gamma-tubulin binding activity. Located in centrosome. [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 ~34.8 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 SPATC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198572.3. 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 | 3 | 1 | 5 | ||
| missense | 6 | 6 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 7 | 3 | 1 | 11 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_940974.2 | 5 | MANE Select | |
| Ensembl | ENSP00000366690.3 | 5 | MANE Select | |
| RefSeq | NP_001127846.1 | 4 | Standard | |
| Ensembl | ENSP00000387613.2 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- cytoplasm
- centrosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000377470
- Coding exons
- 5
- Length
- 15352
- Individuals with no LoFs
- 125311
- Homozygous LoFs
- 7
- Heterozygous LoFs
- 411
- Defined
- 125729
- p
- 0.00166
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0559 | 378 | 375 | 1.01 | 0.0000241 | 3714 |
| Missense (PolyPhen) | 138 | 134.37 | 1.027 | 1349 | ||
| Synonymous | -0.0653 | 175 | 174 | 1.01 | 0.0000123 | 1374 |
| Loss of Function | 0.761 | 15 | 18.5 | 0.809 | 0.00000121 | 168 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0026 | 0.0024 | notable |
| Latino/Admixed American | 0.00060 | 0.00058 | rare |
| Ashkenazi Jewish | 0.00013 | 0.000099 | rare |
| East Asian | 0.0052 | 0.0052 | notable |
| Finnish | 0.00070 | 0.00069 | rare |
| European (Non-Finnish) | 0.00096 | 0.00089 | rare |
| South Asian | 0.0055 | 0.0045 | notable |
| Other | 0.0019 | 0.0016 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0870
Intolerance Scores
- LoFtool
- 0.392
- RVIS EVS
- 0.45
- RVIS percentile EVS
- 78.02
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.282
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |