SPEF1
protein-codingsperm flagellar 1
Gene summary
Enables actin binding activity. Involved in filopodium assembly and lamellipodium assembly. Located in several cellular components, including basolateral plasma membrane; lamellipodium; and microvillus. [provided by Alliance of Genome Resources, Jul 2025]
- C20orf28
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.9 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 SPEF1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015417.5. 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 | 0 | |||||
| missense | 31 | 31 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 31 | 0 | 0 | 31 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056232.2 | 7 | MANE Select | |
| Ensembl | ENSP00000369080.3 | 7 | MANE Select | |
| Ensembl | ENSP00000536681.1 | 7 | Standard | |
| Ensembl | ENSP00000648475.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of microtubule depolymerization
- biological_process
- cell migration
- cilium-dependent cell motility
Molecular Function
- molecular_function
- protein binding
- microtubule binding
Cellular Component
- cellular_component
- cytoplasm
- axoneme
- motile cilium
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000379756
- Coding exons
- 7
- Length
- 3945
- Individuals with no LoFs
- 124792
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 124805
- p
- 0.0000521
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.17 | 100 | 139 | 0.721 | 0.00000720 | 1505 |
| Missense (PolyPhen) | 32 | 47.33 | 0.6761 | 547 | ||
| Synonymous | 1.25 | 47 | 59.3 | 0.793 | 0.00000322 | 460 |
| Loss of Function | 0.972 | 9 | 12.7 | 0.706 | 5.91e-7 | 133 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00027 | 0.00026 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000045 | 0.000044 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Microtubule-associated protein involved in the stabilization of microtubules along the axis of migration during radial intercalation. Promotes the establishment and stabilization of an axis of microtubules required for the active migration of cells into the outer epithelium (By similarity). Microtubule- associated protein that promotes microtubule bundling and stabilizes microtubules against depolymerization in response to cold shock (By similarity). {ECO:0000250|UniProtKB:Q0IH24, ECO:0000250|UniProtKB:Q99JL1}.;
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- LoFtool
- 0.639
- RVIS EVS
- 0.3
- RVIS percentile EVS
- 72.01
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.605
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |