CFAP20

Chr 16AR

cilia and flagella associated protein 20

Also known as: BUG22, C16orf80, EVORF, GTL3, RP107, fSAP23

NCBI Gene: 29105 ENSG00000070761 UniProt: Q9Y6A4 OMIM: 617906

CFAP20 encodes a cilium-specific protein that organizes axonemal structure and regulates ciliary beating through microtubule polyglutamylation. Mutations cause primary ciliary dyskinesia, an autosomal recessive disorder affecting respiratory tract function, fertility, and potentially organ laterality due to defective motile cilia. The gene shows low constraint against loss-of-function variants, consistent with recessive inheritance patterns.

OMIM ResearchSummary from RefSeq, UniProt

Enables RNA binding activity. Involved in several processes, including positive regulation of feeding behavior; protein polyglutamylation; and regulation of cilium beat frequency involved in ciliary motility. Located in microtubule cytoskeleton and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Retinitis pigmentosa 107MIM #621587

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists Retinitis pigmentosa 107; no ClinGen or GenCC tier

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.01

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.01LOEUF

pLI 0.002

Z-score 1.55

OE 0.51 (0.28–1.01)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

2.07Z-score

OE missense 0.47 (0.38–0.58)

56 obs / 119.9 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.51 (0.28–1.01)

0≤0.351.4

Missense OE?0.47 (0.38–0.58)

0≤0.61.4

Synonymous OE?0.89

0≤1.21.6

LoF obs/exp: 6 / 11.7Missense obs/exp: 56 / 119.9Syn Z: 0.55

Background carrier burden — how many people carry a rare variant somewhere in CFAP20?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 720

198 rare PASS variants

Rare truncating (LoF)

1 in 3,200

40 rare PASS variants

Rare synonymous (reference)

1 in 740

74 rare PASS variants

Rare missense and truncating variants are carried at similar rates in CFAP20; 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 690	1 in 4,100
South Asian	~43k	1 in 570	1 in 1,100
Remaining (unassigned)	~30k	1 in 490	1 in 840
European (Finnish)	~27k	1 in 2,100	1 in 1,200
Admixed American	~22k	1 in 970	none seen
African / African American	~21k	1 in 650	≈ 1 in 6,400
East Asian	~20k	1 in 1,300	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 1,500	none seen
Middle Eastern	~2,884	1 in 320	none seen

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.

Exome coverage (gnomAD): All 6 coding exons well covered in gnomAD exomes and genomes.? see exons ↓