CFAP96

Chr 4

cilia and flagella associated protein 96

Also known as: C4orf47

NCBI Gene: 441054 ENSG00000205129 UniProt: A7E2U8

The protein localizes to non-motile cilia, centrosomes, and cytoplasmic microtubules where it likely functions in ciliary structure or signaling. Mutations cause autosomal recessive retinal dystrophy and Bardet-Biedl syndrome, ciliopathies that can present with vision loss, obesity, kidney dysfunction, and developmental delays. The gene shows minimal constraint against loss-of-function variants, consistent with recessive inheritance where one functional copy is insufficient.

ResearchSummary from RefSeq

Located in 9+0 non-motile cilium; centrosome; and cytoplasmic microtubule. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.02

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.02LOEUF

pLI 0.001

Z-score 1.53

OE 0.54 (0.31–1.02)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.23Z-score

OE missense 0.71 (0.60–0.84)

101 obs / 142.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.54 (0.31–1.02)

0≤0.351.4

Missense OE?0.71 (0.60–0.84)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 7 / 12.9Missense obs/exp: 101 / 142.5Syn Z: 0.02

Background carrier burden — how many people carry a rare variant somewhere in CFAP96?

gnomAD v4 · ~700k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

366 rare PASS variants

Rare truncating (LoF)

1 in 340

86 rare PASS variants

Rare synonymous (reference)

1 in 130

145 rare PASS variants

Rare missense and truncating variants are carried at similar rates in CFAP96; 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)	~539k	1 in 130	1 in 750
South Asian	~40k	1 in 150	1 in 590
Remaining (unassigned)	~29k	1 in 99	1 in 450
European (Finnish)	~25k	1 in 1,600	1 in 4,900
African / African American	~21k	1 in 100	1 in 460
East Asian	~18k	1 in 120	1 in 710
Admixed American	~18k	1 in 140	1 in 350
Ashkenazi Jewish	~13k	1 in 1,400	1 in 1,400
Middle Eastern	~2,850	1 in 140	1 in 250

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.