SPATC1L
protein-codingspermatogenesis and centriole associated 1 like
Gene summary
Enables identical protein binding activity. Predicted to be involved in spermatogenesis. Predicted to act upstream of or within actin polymerization or depolymerization; positive regulation of cAMP-dependent protein kinase activity; and positive regulation of cAMP/PKA signal transduction. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2025]
- C21orf56
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~23.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0005365
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0005365
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SPATC1L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001142854.2. 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 | 1 | 3 | |||
| missense | 81 | 4 | 1 | 86 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 84 | 5 | 1 | 90 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001136326.1 | 4 | MANE Select | |
| Ensembl | ENSP00000291672.5 | 4 | MANE Select | |
| RefSeq | NP_115637.3 | 3 | Standard | |
| Ensembl | ENSP00000333869.6 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- biological_process
Molecular Function
- molecular_function
- protein binding
Cellular Component
- cellular_component
- centrosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000291672
- Coding exons
- 4
- Length
- 23329
- Individuals with no LoFs
- 125444
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 49
- Defined
- 125493
- p
- 0.000195
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.291 | 199 | 211 | 0.944 | 0.0000156 | 2152 |
| Missense (PolyPhen) | 73 | 75.206 | 0.97066 | 780 | ||
| Synonymous | -1.84 | 136 | 111 | 1.22 | 0.00000940 | 726 |
| Loss of Function | -0.488 | 11 | 9.39 | 1.17 | 4.80e-7 | 110 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00033 | 0.00031 | rare |
| Latino/Admixed American | 0.00047 | 0.00046 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000098 | 0.000092 | rare |
| European (Non-Finnish) | 0.000092 | 0.000079 | rare |
| South Asian | 0.00037 | 0.00036 | rare |
| Other | 0.00036 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- RVIS EVS
- 1.2
- RVIS percentile EVS
- 92.92
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |