SAXO1
Basic information
Region (hg38): 9:18858906-19049358
Previous symbols: [ "C9orf138", "FAM154A" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (107 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAXO1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000153707.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 103 | 107 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 103 | 5 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SAXO1 | protein_coding | protein_coding | ENST00000380534 | 4 | 105596 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.30e-21 | 0.0000663 | 125083 | 4 | 661 | 125748 | 0.00265 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -2.70 | 402 | 276 | 1.46 | 0.0000152 | 3111 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0124 | 0.0123 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00995 | 0.00994 |
Finnish | 0.000185 | 0.000185 |
European (Non-Finnish) | 0.00143 | 0.00142 |
Middle Eastern | 0.00995 | 0.00994 |
South Asian | 0.000850 | 0.000817 |
Other | 0.00147 | 0.00147 |
dbNSFP
Source:
- Function
- FUNCTION: May play a role in the regulation of cilium length. Stabilizes microtubules at low temperature. {ECO:0000269|PubMed:25673876}.;
Intolerance Scores
- loftool
- rvis_EVS
- 2.36
- rvis_percentile_EVS
- 98.43
Haploinsufficiency Scores
- pHI
- 0.176
- hipred
- N
- hipred_score
- 0.123
- ghis
Essentials
- essential_gene_CRISPR
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Mouse Genome Informatics
- Gene name
- Saxo1
- Phenotype
Gene ontology
- Biological process
- cold acclimation;cell projection organization;microtubule anchoring;positive regulation of cilium assembly;protein stabilization;cellular response to cold
- Cellular component
- centriole;cytoskeleton;axonemal microtubule;motile cilium;ciliary basal body;sperm flagellum
- Molecular function
- protein binding;microtubule binding