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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			70	4		74
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			37	4	2	43
Total	0	0	107	9	2

Variants in SAXO1

This is a list of pathogenic ClinVar variants found in the SAXO1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-18887861-A-G		not specified	Uncertain significance (Feb 17, 2022)
9-18887874-T-C			Likely benign (Jul 01, 2022)
9-18887912-C-T		not specified	Uncertain significance (Jan 07, 2022)
9-18887937-G-C		not specified	Uncertain significance (Jun 07, 2023)
9-18887960-G-C		not specified	Uncertain significance (Jan 07, 2025)
9-18887962-G-A		ADAMTSL1-related disorder	Likely benign (Feb 01, 2022)
9-18887996-A-G		ADAMTSL1-related disorder	Likely benign (Dec 29, 2022)
9-18888010-G-A		not specified	Likely benign (Jul 06, 2021)
9-18888018-G-A		not specified	Uncertain significance (Jul 30, 2023)
9-18888039-C-G		not specified	Uncertain significance (Aug 02, 2021)
9-18889586-A-G		not specified	Uncertain significance (May 13, 2024)
9-18889622-G-A		not specified	Uncertain significance (Apr 08, 2024)
9-18889643-T-G		not specified	Uncertain significance (Jun 09, 2022)
9-18889651-C-G		not specified	Uncertain significance (Jan 24, 2025)
9-18889662-C-G		not specified	Uncertain significance (Jan 09, 2024)
9-18889673-A-G		ADAMTSL1-related disorder • not specified	Likely benign (Jun 23, 2021)
9-18889678-G-A		not specified	Likely benign (Feb 11, 2025)
9-18889706-C-T		not specified	Uncertain significance (Feb 24, 2025)
9-18889711-C-G		not specified	Uncertain significance (Dec 06, 2021)
9-18889721-C-T		not specified	Uncertain significance (Jan 19, 2024)
9-18892409-C-T		not specified	Uncertain significance (Jan 28, 2025)
9-18892429-G-T		not specified	Uncertain significance (May 16, 2024)
9-18892436-G-A		not specified	Uncertain significance (Apr 12, 2024)
9-18892448-G-A		not specified	Uncertain significance (Dec 07, 2023)
9-18892448-G-T		not specified	Uncertain significance (Dec 21, 2023)

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