SAXO1
protein-codingstabilizer of axonemal microtubules 1
Gene summary
Enables microtubule binding activity. Involved in several processes, including cold acclimation; positive regulation of cilium assembly; and protein stabilization. Located in microtubule cytoskeleton and sperm flagellum. [provided by Alliance of Genome Resources, Jul 2025]
- C9orf138
- FAM154A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~190.5 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 SAXO1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_153707.4. 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 | 113 | 7 | 120 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 114 | 8 | 0 | 122 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_714918.2 | 4 | MANE Select | |
| Ensembl | ENSP00000369907.4 | 4 | MANE Select | |
| RefSeq | NP_001273978.1 | 3 | Standard | |
| RefSeq | NP_001273979.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cold acclimation
- cell projection organization
- microtubule anchoring
- positive regulation of cilium assembly
- protein stabilization
Molecular Function
- protein binding
- microtubule binding
Cellular Component
- centriole
- cytoskeleton
- axonemal microtubule
- motile cilium
- ciliary basal body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000380534
- Coding exons
- 4
- Length
- 105596
- Individuals with no LoFs
- 125083
- Homozygous LoFs
- 4
- Heterozygous LoFs
- 661
- Defined
- 125748
- p
- 0.00265
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -2.70 | 402 | 276 | 1.46 | 0.0000152 | 3111 |
| Missense (PolyPhen) | 126 | 87.547 | 1.4392 | 1068 | ||
| Synonymous | -1.80 | 124 | 101 | 1.23 | 0.00000553 | 908 |
| Loss of Function | -1.63 | 27 | 19.3 | 1.40 | 0.00000119 | 212 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0078 | 0.0076 | notable |
| Latino/Admixed American | 0.0047 | 0.0047 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.010 | 0.0099 | notable |
| Finnish | 0.00018 | 0.00018 | rare |
| European (Non-Finnish) | 0.0014 | 0.0014 | notable |
| South Asian | 0.00085 | 0.00082 | rare |
| Other | 0.0015 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in the regulation of cilium length. Stabilizes microtubules at low temperature. {ECO:0000269|PubMed:25673876}.;
Intolerance Scores
- RVIS EVS
- 2.36
- RVIS percentile EVS
- 98.43
Essentials
- Essential (gene trap)
- N