CFAP90

Chr 5

cilia and flagella associated protein 90

Also known as: C5orf49

NCBI Gene: 134121 ENSG00000215217 UniProt: A4QMS7

CFAP90 encodes a microtubule inner protein that is essential for motile cilia beating in the ciliary axoneme. Mutations cause primary ciliary dyskinesia with autosomal recessive inheritance, affecting respiratory function, fertility, and potentially laterality determination. The gene shows low constraint to loss-of-function variation, consistent with the recessive inheritance pattern observed in ciliopathies.

ResearchSummary from RefSeq, UniProt

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

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.70

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.70LOEUF

pLI 0.012

Z-score 0.48

OE 0.74 (0.33–1.70)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.11Z-score

OE missense 0.96 (0.80–1.17)

73 obs / 75.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.74 (0.33–1.70)

0≤0.351.4

Missense OE?0.96 (0.80–1.17)

0≤0.61.4

Synonymous OE?0.81

0≤1.21.6

LoF obs/exp: 3 / 4.0Missense obs/exp: 73 / 75.8Syn Z: 0.82

Background carrier burden — how many people carry a rare variant somewhere in CFAP90?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 230

224 rare PASS variants

Rare truncating (LoF)

1 in 3,300

33 rare PASS variants

Rare synonymous (reference)

1 in 860

87 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CFAP90. 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 330	1 in 3,300
South Asian	~43k	1 in 130	1 in 8,000
Remaining (unassigned)	~30k	1 in 160	1 in 4,700
European (Finnish)	~27k	1 in 190	≈ 1 in 8,500
Admixed American	~22k	1 in 160	1 in 3,500
African / African American	~21k	1 in 220	1 in 1,300
East Asian	~20k	1 in 290	≈ 1 in 5,900
Ashkenazi Jewish	~13k	1 in 470	none seen
Middle Eastern	~2,884	1 in 140	≈ 1 in 1,400

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): 1 of 3 coding exons well covered in gnomAD exomes; exons 1, 2 marginal. Genomes: all 3.? see exons ↓