SAXO1

Summary

SAXO1 (stabilizer of axonemal microtubules 1, HGNC:28566) is a protein-coding gene on chromosome 9p22.1, encoding Stabilizer of axonemal microtubules 1 (Q8IYX7). May play a role in the regulation of cilium length.

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.

Source: NCBI Gene 158297 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 126 total — 1 pathogenic
• MANE Select transcript: NM_153707

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28566
Approved symbol	SAXO1
Name	stabilizer of axonemal microtubules 1
Location	9p22.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC35182
Ensembl gene	ENSG00000155875
Ensembl biotype	protein_coding
OMIM	616292
Entrez	158297

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000380530, ENST00000380534, ENST00000542071, ENST00000583128, ENST00000649457

RefSeq mRNA: 3 — MANE Select: NM_153707 NM_001287049, NM_001287050, NM_153707

CCDS: CCDS6487, CCDS75819, CCDS75820

Canonical transcript exons

ENST00000380534 — 4 exons

Exon	Start	End
ENSE00001023212	18941637	18941839
ENSE00001485365	18927650	18929055
ENSE00001485372	19032871	19033209
ENSE00003613198	18950758	18950937

Expression profiles

Bgee: expression breadth broad, 57 present calls, max score 95.35.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2245 / max 439.6829, expressed in 381 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
100144	0.5748	276
100143	0.5435	81
100141	0.0720	3
100142	0.0262	3
100140	0.0080	3

Top tissues by expression

199 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	95.35	gold quality
oocyte	CL:0000023	93.89	gold quality
left testis	UBERON:0004533	89.27	gold quality
right testis	UBERON:0004534	88.74	gold quality
testis	UBERON:0000473	86.48	gold quality
sperm	CL:0000019	79.64	gold quality
adult organism	UBERON:0007023	77.89	gold quality
buccal mucosa cell	CL:0002336	70.62	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	69.13	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	68.69	gold quality
tendon of biceps brachii	UBERON:0008188	64.24	gold quality
nasal cavity epithelium	UBERON:0005384	58.71	gold quality
superficial temporal artery	UBERON:0001614	58.70	gold quality
parietal pleura	UBERON:0002400	58.65	gold quality
visceral pleura	UBERON:0002401	58.29	gold quality
cartilage tissue	UBERON:0002418	56.81	gold quality
seminal vesicle	UBERON:0000998	56.78	gold quality
myocardium	UBERON:0002349	56.57	gold quality
epithelium of mammary gland	UBERON:0003244	56.52	gold quality
mammary duct	UBERON:0001765	56.51	gold quality
mucosa of paranasal sinus	UBERON:0005030	56.00	gold quality
tibialis anterior	UBERON:0001385	55.81	silver quality
upper arm skin	UBERON:0004263	55.64	gold quality
pancreatic ductal cell	CL:0002079	55.43	silver quality
tibia	UBERON:0000979	55.20	gold quality
sural nerve	UBERON:0015488	55.02	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.90	gold quality
lateral globus pallidus	UBERON:0002476	54.78	gold quality
tendon	UBERON:0000043	54.61	silver quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting SAXO1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-10523-5P	99.91	69.22	2038
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-892A	99.54	68.16	1141
HSA-MIR-5571-5P	99.49	66.99	1764
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-6770-5P	98.97	66.76	1853
HSA-MIR-518C-5P	98.53	69.20	1640
HSA-MIR-5691	98.23	67.02	1335
HSA-MIR-6805-3P	98.23	67.02	1334
HSA-MIR-12126	98.09	64.82	637
HSA-MIR-1278	97.75	67.55	628
HSA-MIR-890	97.47	68.67	982

Literature-anchored findings (GeneRIF, showing 2)

• Single-nucleotide polymorphisms in FAM154A is associiated with non-small cell lung cancer. (PMID:23144319)
• SAXO1 binds specifically to centriole and cilium microtubules. (PMID:25673876)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
mus_musculus	Saxo1	ENSMUSG00000028492
mus_musculus	Gm15229	ENSMUSG00000085880
rattus_norvegicus	Saxo1	ENSRNOG00000048197
drosophila_melanogaster	CG7131	FBGN0038598
caenorhabditis_elegans		WBGENE00010357
caenorhabditis_elegans	T08G11.3	WBGENE00011630
caenorhabditis_elegans		WBGENE00044142

Paralogs (1): SAXO2 (ENSG00000188659)

Protein

Protein identifiers

Stabilizer of axonemal microtubules 1 — Q8IYX7 (reviewed: Q8IYX7)

All UniProt accessions (3): Q8IYX7, F6S232, Q5VZT6

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in the regulation of cilium length. Stabilizes microtubules at low temperature.

Subunit / interactions. Associates with microtubules via the Mn regions.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriole. Cilium basal body. Cilium axoneme. Flagellum axoneme.

Tissue specificity. Widely expressed, with highest levels in testis. Expressed in mature spermatozoa (at protein level).

Domain organisation. The Mn regions are involved in microtubule-binding and stabilization at low temperature. They are required and sufficient for cilium targeting. The N-terminal region (residues 1-29) might play a role in centriole retention.

Similarity. Belongs to the FAM154 family.

RefSeq proteins (3): NP_001273978, NP_001273979, NP_714918* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR033336	SAXO1/2	Family

Pfam: PF05217

UniProt features (19 total): region of interest 13, sequence variant 3, chain 1, compositionally biased region 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IYX7-F1	67.51	0.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (1):

Position	Phenotype
116–119	no effect on subcellular location.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 97 (showing top): GOBP_RESPONSE_TO_COLD, TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOCC_MICROTUBULE_ORGANIZING_CENTER, YGACNNYACAR_UNKNOWN, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_CILIUM_ORGANIZATION, GOBP_PROTEIN_STABILIZATION, GOCC_CENTROSOME, GOBP_ORGANELLE_ASSEMBLY, GOBP_REGULATION_OF_PROTEIN_STABILITY, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_REGULATION_OF_CILIUM_ASSEMBLY

GO Biological Process (5): cold acclimation (GO:0009631), cell projection organization (GO:0030030), positive regulation of cilium assembly (GO:0045724), protein stabilization (GO:0050821), cellular response to cold (GO:0070417)

GO Molecular Function (2): microtubule binding (GO:0008017), protein binding (GO:0005515)

GO Cellular Component (10): centrosome (GO:0005813), centriole (GO:0005814), cytoskeleton (GO:0005856), axonemal microtubule (GO:0005879), motile cilium (GO:0031514), ciliary basal body (GO:0036064), sperm flagellum (GO:0036126), cytoplasm (GO:0005737), cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
microtubule organizing center	3
response to cold	2
intracellular membraneless organelle	2
cilium	2
cellular anatomical structure	2
cellular component organization	1
cilium assembly	1
positive regulation of plasma membrane bounded cell projection assembly	1
regulation of cilium assembly	1
positive regulation of organelle assembly	1
regulation of protein stability	1
cellular response to stress	1
tubulin binding	1
binding	1
centriole	1
cytoplasmic microtubule	1
axoneme	1
9+2 motile cilium	1
intracellular anatomical structure	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

861 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SAXO1	C10orf120	Q5SQS8	615
SAXO1	MAP6D1	Q9H9H5	612
SAXO1	C5orf47	Q569G3	587
SAXO1	CCDC27	Q2M243	539
SAXO1	CBY3	A6NI87	495
SAXO1	CEP162	Q5TB80	494
SAXO1	LYPD4	Q6UWN0	479
SAXO1	DRC11	Q86XH1	475
SAXO1	TRIM42	Q8IWZ5	468
SAXO1	CEP120	Q8N960	468
SAXO1	PP2D1	A8MPX8	456
SAXO1	SPINT4	Q6UDR6	445
SAXO1	ZPLD1	Q8TCW7	425
SAXO1	CBY2	Q8NA61	418
SAXO1	ZPBP2	Q6X784	393

IntAct

180 interactions, top by confidence:

A	B	Type	Score
FHL3	SAXO1	psi-mi:“MI:0915”(physical association)	0.780
SAXO1	ACTN2	psi-mi:“MI:0915”(physical association)	0.780
ACTN2	SAXO1	psi-mi:“MI:0915”(physical association)	0.780
SAXO1	FHL3	psi-mi:“MI:0915”(physical association)	0.780
SAXO1	STK16	psi-mi:“MI:0915”(physical association)	0.720
ZMYND19	SAXO1	psi-mi:“MI:0915”(physical association)	0.720
SAXO1	ZMYND19	psi-mi:“MI:0915”(physical association)	0.720
STK16	SAXO1	psi-mi:“MI:0915”(physical association)	0.720
LMO2	SAXO1	psi-mi:“MI:0915”(physical association)	0.670
SAXO1	FHL2	psi-mi:“MI:0915”(physical association)	0.670
SAXO1	LMO2	psi-mi:“MI:0915”(physical association)	0.670
FHL2	SAXO1	psi-mi:“MI:0915”(physical association)	0.670
Hoxa1	SAXO1	psi-mi:“MI:0915”(physical association)	0.570

BioGRID (61): FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid), FAM154A (Two-hybrid)

ESM2 similar proteins: A0A3Q1N1R0, A1A5R9, A2AVQ5, A3KGF7, A3KQA5, A4IH24, A5WUY6, B1H283, D4A1F2, E1BKH1, E7F9T0, F1RA39, O70209, O70400, O89040, P30944, P52944, P55292, Q00722, Q08BC4, Q2TBH0, Q2TBS4, Q32TF8, Q32TG3, Q3KQ80, Q3SX64, Q3SYZ8, Q3TZ65, Q4KLY8, Q4R7D3, Q5EB30, Q5JST6, Q5JVL4, Q5M8M2, Q6AYP6, Q6NUF4, Q810P2, Q8AVY1, Q8C8J0, Q8IXM7

Diamond homologs: Q4R7D3, Q658L1, Q6AYP6, Q8BQB6, Q8IYX7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

126 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	113
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1703570	GRCh37/hg19 9p24.3-q13(chr9:203861-67986965)	Pathogenic

SpliceAI

2450 predictions. Top by Δscore:

Variant	Effect	Δscore
9:18929052:TCAG:T	acceptor_gain	1.0000
9:18929053:CAG:C	acceptor_gain	1.0000
9:18929053:CAGC:C	acceptor_gain	1.0000
9:18929056:C:CC	acceptor_gain	1.0000
9:18941683:A:AC	donor_gain	1.0000
9:18941684:C:CC	donor_gain	1.0000
9:18950752:CCTCA:C	donor_loss	1.0000
9:18950754:TCA:T	donor_loss	1.0000
9:18950755:CACCT:C	donor_loss	1.0000
9:18950756:A:C	donor_loss	1.0000
9:18950757:C:A	donor_loss	1.0000
9:18950934:CCGC:C	acceptor_gain	1.0000
9:18950935:CGC:C	acceptor_gain	1.0000
9:18950935:CGCC:C	acceptor_gain	1.0000
9:18950938:C:T	acceptor_loss	1.0000
9:18989904:C:CT	acceptor_gain	1.0000
9:18989905:A:T	acceptor_gain	1.0000
9:18887825:TTCTA:T	acceptor_loss	0.9900
9:18887827:CTA:C	acceptor_loss	0.9900
9:18887828:TAGGC:T	acceptor_loss	0.9900
9:18887829:A:AG	acceptor_gain	0.9900
9:18887830:G:GG	acceptor_gain	0.9900
9:18887830:G:GT	acceptor_loss	0.9900
9:18887830:GGCT:G	acceptor_gain	0.9900
9:18889749:G:GG	donor_gain	0.9900
9:18892593:CCAG:C	donor_loss	0.9900
9:18892596:GG:G	donor_loss	0.9900
9:18892598:T:C	donor_loss	0.9900
9:18905780:A:AG	acceptor_gain	0.9900
9:18905781:G:GG	acceptor_gain	0.9900

AlphaMissense

3127 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:18928241:A:C	F412L	0.973
9:18928241:A:T	F412L	0.973
9:18928243:A:G	F412L	0.973
9:18928863:G:A	T205I	0.958
9:19032880:C:G	C10S	0.953
9:19032881:A:T	C10S	0.953
9:18928150:A:C	Y443D	0.952
9:18950926:C:G	C17S	0.950
9:18950927:A:T	C17S	0.950
9:18950927:A:G	C17R	0.949
9:18928655:A:C	F274L	0.948
9:18928655:A:T	F274L	0.948
9:18928657:A:G	F274L	0.948
9:19032889:C:G	C7S	0.948
9:19032890:A:T	C7S	0.948
9:18928563:G:A	T305I	0.947
9:18941830:A:C	F76L	0.947
9:18941830:A:T	F76L	0.947
9:18941832:A:G	F76L	0.947
9:18950931:A:C	H15Q	0.945
9:18950931:A:T	H15Q	0.945
9:19032879:G:C	C10W	0.945
9:19032881:A:G	C10R	0.944
9:18950925:A:C	C17W	0.939
9:19032896:A:G	C5R	0.939
9:18928218:C:G	C420S	0.938
9:18928219:A:G	C420R	0.938
9:18928219:A:T	C420S	0.938
9:19032895:C:G	C5S	0.937
9:19032896:A:T	C5S	0.937

dbSNP variants (sampled 300 via entrez): RS1000005262 (9:18963011 G>A), RS1000025396 (9:18934071 A>G), RS1000037680 (9:18992435 G>C), RS1000078931 (9:18933998 A>G), RS1000093347 (9:18996518 T>C), RS1000117898 (9:18929986 A>C,G), RS1000121204 (9:18974403 G>A), RS1000128396 (9:19024373 A>G), RS1000163981 (9:19020718 G>A,C), RS1000186092 (9:19010475 T>A,C,G), RS1000204275 (9:18955470 G>A), RS1000204857 (9:18963191 G>A,T), RS1000229298 (9:18988522 A>T), RS1000235210 (9:19001151 T>C), RS1000236171 (9:19006620 G>A,T)

Disease associations

OMIM: gene MIM:616292 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): tetrasomy 9p (MONDO:0018030)

Orphanet (1): Tetrasomy 9p syndrome (Orphanet:3310)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001734_3	Non-small cell lung cancer	2.000000e-07
GCST004639_12	Prudent dietary pattern	3.000000e-06
GCST012187_1	Cardiovascular event in colchicine-treated recent myocardial infarction (time to event)	6.000000e-08

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement
EFO:0006919	cardiovascular event measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C538027	Chromosome 9, tetrasomy 9p (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
methyleugenol	decreases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
sodium arsenite	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Benzo(a)pyrene	affects methylation	1
Copper	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression	1
Thapsigargin	increases expression	1
Permethrin	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.