SAXO2

protein-coding

stabilizer of axonemal microtubules 2

Gene summary

Predicted to enable microtubule binding activity. Predicted to be active in microtubule cytoskeleton and sperm flagellum. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM154B

MANE transcript

NM_001348699.2

Inheritance

—

ClinVar variants

U:75B:5

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 1.22

Max pathogenic AF

—

Genomic locus

chr15:82,262,810-82,284,930

External References & Databases

Ensembl (ENSG00000188659)

Transcript & Mutation Effects

hg38 • Region Span ~22.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SAXO2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 74

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001348699.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			73 clinvar	5 clinvar		78
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	75	5	0	80

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001348699.2	RefSeq	NP_001335628.1	4	MANE Select
ENST00000682753.1	Ensembl	ENSP00000508095.1	4	MANE Select
NM_001008226.2	RefSeq	NP_001008227.1	3	Standard
NM_001348700.2	RefSeq	NP_001335629.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule anchoring

Molecular Function

microtubule binding

Cellular Component

centriole
cytoskeleton
axonemal microtubule
motile cilium
ciliary basal body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000339465
Coding exons: 3
Length: 22121
Individuals with no LoFs: 124218
Homozygous LoFs: 8
Heterozygous LoFs: 1522
Defined: 125748
p: 0.00610

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.205	228	219	1.04	0.0000115	2644
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0033	0.0033	notable
Latino/Admixed American	0.0022	0.0022	notable
Ashkenazi Jewish	0.0035	0.0035	notable
East Asian	0.00051	0.00049	rare
Finnish	0.013	0.013	notable
European (Non-Finnish)	0.0090	0.0090	notable
South Asian	0.00072	0.00072	rare
Other	0.0065	0.0064	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.89
RVIS percentile EVS: 89.19

Essentials

Essential (gene trap): N