SPATA4

Chr 4

spermatogenesis associated 4

Also known as: CFAP178, FAP178, SPEF1B, TSARG2

NCBI Gene: 132851 ENSG00000150628 UniProt: Q8NEY3 OMIM: 609879

The protein is predicted to bind microtubules and regulate cytoskeleton organization, and may play a role in apoptosis regulation. Mutations cause primary ciliary dyskinesia with or without situs inversus in an autosomal recessive inheritance pattern. This gene shows minimal constraint against loss-of-function variants.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable microtubule binding activity. Predicted to be involved in regulation of cytoskeleton organization. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.51

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.51LOEUF

pLI 0.000

Z-score 0.11

OE 0.97 (0.64–1.51)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.32Z-score

OE missense 1.07 (0.94–1.22)

171 obs / 159.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.97 (0.64–1.51)

0≤0.351.4

Missense OE?1.07 (0.94–1.22)

0≤0.61.4

Synonymous OE?0.80

0≤1.21.6

LoF obs/exp: 14 / 14.5Missense obs/exp: 171 / 159.7Syn Z: 1.22

Background carrier burden — how many people carry a rare variant somewhere in SPATA4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 170

428 rare PASS variants

Rare truncating (LoF)

1 in 170

74 rare PASS variants

Rare synonymous (reference)

1 in 230

136 rare PASS variants

Rare missense and truncating variants are carried at similar rates in SPATA4; 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 320	1 in 260
South Asian	~43k	1 in 97	1 in 1,600
Remaining (unassigned)	~30k	1 in 140	1 in 200
European (Finnish)	~27k	1 in 780	1 in 3,000
Admixed American	~22k	1 in 220	1 in 740
African / African American	~21k	1 in 95	1 in 460
East Asian	~20k	1 in 130	1 in 960
Ashkenazi Jewish	~13k	1 in 470	1 in 1,500
Middle Eastern	~2,884	1 in 180	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.