SAXO1

Chr 9

stabilizer of axonemal microtubules 1

Also known as: C9orf138, FAM154A

NCBI Gene: 158297 ENSG00000155875 UniProt: Q8IYX7 OMIM: 616292

The SAXO1 protein binds to and stabilizes microtubules, particularly at low temperatures, and regulates cilium length. Mutations cause autosomal recessive primary ciliary dyskinesia with intellectual disability and developmental delay, affecting the respiratory system and neurodevelopment. This gene is not highly constrained against loss-of-function variants.

OMIM ResearchSummary from RefSeq, UniProt

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. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.85

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.85LOEUF

pLI 0.000

Z-score -1.63

OE 1.40 (1.03–1.85)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-2.70Z-score

OE missense 1.46 (1.34–1.58)

402 obs / 275.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.40 (1.03–1.85)

0≤0.351.4

Missense OE?1.46 (1.34–1.58)

0≤0.61.4

Synonymous OE?1.23

0≤1.21.6

LoF obs/exp: 27 / 19.3Missense obs/exp: 402 / 275.7Syn Z: -1.80

Background carrier burden — how many people carry a rare variant somewhere in SAXO1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 68

880 rare PASS variants

Rare truncating (LoF)

1 in 260

113 rare PASS variants

Rare synonymous (reference)

1 in 170

287 rare PASS variants

Rare missense and truncating variants are carried at similar rates in SAXO1; this gene does not show strong loss-of-function constraint by this measure. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 96	1 in 330
South Asian	~43k	1 in 49	1 in 500
Remaining (unassigned)	~30k	1 in 48	1 in 220
European (Finnish)	~27k	1 in 210	1 in 2,700
Admixed American	~22k	1 in 53	1 in 400
African / African American	~21k	1 in 39	1 in 550
East Asian	~20k	1 in 72	1 in 350
Ashkenazi Jewish	~13k	1 in 260	1 in 1,600
Middle Eastern	~2,884	1 in 51	1 in 480

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 4 coding exons well covered in gnomAD exomes and genomes.? see exons ↓