SAXO4

Chr 11

stabilizer of axonemal microtubules 4

Also known as: C11orf66, IIIG9, PPP1R32

NCBI Gene: 220004 ENSG00000162148 UniProt: Q7Z5V6 OMIM: 619047

The SAXO4 protein enables phosphatase binding and is involved in flagellated sperm motility, located in the ciliary basal body. Mutations in this gene cause primary ciliary dyskinesia with autosomal recessive inheritance. This gene shows tolerance to loss-of-function variants (LOEUF 1.27), and the ciliary dysfunction typically affects respiratory and reproductive systems.

OMIM ResearchSummary from RefSeq

Enables phosphatase binding activity. Predicted to be involved in flagellated sperm motility. Located in ciliary basal body. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.27

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.27LOEUF

pLI 0.000

Z-score 0.46

OE 0.90 (0.65–1.27)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.02Z-score

OE missense 1.00 (0.90–1.10)

258 obs / 258.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.90 (0.65–1.27)

0≤0.351.4

Missense OE?1.00 (0.90–1.10)

0≤0.61.4

Synonymous OE?0.85

0≤1.21.6

LoF obs/exp: 24 / 26.6Missense obs/exp: 258 / 258.8Syn Z: 1.18

Background carrier burden — how many people carry a rare variant somewhere in SAXO4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 66

604 rare PASS variants

Rare truncating (LoF)

1 in 400

128 rare PASS variants

Rare synonymous (reference)

1 in 210

227 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SAXO4. 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 90	1 in 470
South Asian	~43k	1 in 73	1 in 880
Remaining (unassigned)	~30k	1 in 66	1 in 310
European (Finnish)	~27k	1 in 160	1 in 1,300
Admixed American	~22k	1 in 59	1 in 410
African / African American	~21k	1 in 61	1 in 400
East Asian	~20k	1 in 97	1 in 240
Ashkenazi Jewish	~13k	1 in 200	≈ 1 in 4,100
Middle Eastern	~2,884	1 in 69	1 in 470

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.