SAXO1

stabilizer of axonemal microtubules 1

Basic information

Region (hg38): 9:18858906-19049358

Previous symbols: [ "C9orf138", "FAM154A" ]

Links

ENSG00000155875 ∙ NCBI:158297 ∙ OMIM:616292 ∙ HGNC:28566 ∙ Uniprot:Q8IYX7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAXO1 gene.

• 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			103	4		107
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	103	5	0

GnomAD

Source: gnomAD

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: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Saxo1

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