SAXO2

stabilizer of axonemal microtubules 2

Basic information

Region (hg38): 15:82262810-82284930

Previous symbols: [ "FAM154B" ]

Links

ENSG00000188659 ∙ NCBI:283726 ∙ ∙ HGNC:33727 ∙ Uniprot:Q658L1 ∙ 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 SAXO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAXO2 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						0
missense			33	2		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	2	0

Variants in SAXO2

This is a list of pathogenic ClinVar variants found in the SAXO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-82262929-G-A		not specified	Uncertain significance (Jun 16, 2023)
15-82271605-C-T		not specified	Likely benign (Mar 03, 2025)
15-82271625-A-T		not specified	Uncertain significance (Feb 12, 2024)
15-82271635-A-G		not specified	Uncertain significance (Jul 13, 2022)
15-82271670-C-G		not specified	Uncertain significance (Aug 30, 2021)
15-82271689-G-T		not specified	Uncertain significance (Mar 30, 2024)
15-82271697-T-C		not specified	Uncertain significance (Jan 09, 2025)
15-82271704-G-A		not specified	Uncertain significance (Dec 04, 2024)
15-82271746-G-A		not specified	Uncertain significance (Mar 29, 2022)
15-82271764-T-C		not specified	Uncertain significance (Feb 06, 2025)
15-82271766-A-G		not specified	Uncertain significance (Sep 04, 2024)
15-82271779-T-C		not specified	Uncertain significance (Dec 17, 2021)
15-82271793-A-C		not specified	Uncertain significance (Jun 29, 2023)
15-82282125-A-G		not specified	Uncertain significance (Jan 31, 2024)
15-82282154-C-T		not specified	Uncertain significance (May 21, 2024)
15-82282182-C-T		not specified	Uncertain significance (Feb 12, 2025)
15-82282197-T-C		not specified	Uncertain significance (Nov 07, 2022)
15-82282211-A-G		not specified	Uncertain significance (Mar 01, 2025)
15-82282220-G-A		not specified	Uncertain significance (Jan 20, 2025)
15-82282257-G-A		not specified	Uncertain significance (Nov 15, 2024)
15-82282268-T-G		not specified	Uncertain significance (Sep 15, 2021)
15-82282271-T-C		not specified	Likely benign (Nov 21, 2023)
15-82282283-C-T		not specified	Uncertain significance (Apr 07, 2022)
15-82282319-C-T		not specified	Uncertain significance (Nov 10, 2024)
15-82282347-A-T		not specified	Uncertain significance (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAXO2	protein_coding	protein_coding	ENST00000339465	3	22121

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.33e-11	0.0218	124218	8	1522	125748	0.00610

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.205	228	219	1.04	0.0000115	2644
Missense in Polyphen		59	58.031	1.0167		726
Synonymous	0.283	69	72.1	0.958	0.00000350	738
Loss of Function	-0.696	14	11.5	1.22	4.81e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00550	0.00550
Ashkenazi Jewish	0.00347	0.00348
East Asian	0.000509	0.000489
Finnish	0.0131	0.0131
European (Non-Finnish)	0.00899	0.00895
Middle Eastern	0.000509	0.000489
South Asian	0.000719	0.000719
Other	0.00652	0.00637

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.19

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.167
• ghis: 0.389

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Saxo2

Gene ontology

• Biological process: microtubule anchoring
• Cellular component: centriole;cytoskeleton;axonemal microtubule;motile cilium;ciliary basal body;sperm flagellum
• Molecular function: microtubule binding