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…

LOEUF 1.02

Clinical Summary— CFAP96

⚡

Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

📋

ClinVar Variants

2 unique Pathogenic / Likely Pathogenic· 47 VUS of 77 total submissions

Explore recent and relevant literature in Research Assistant →

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

ClinVar Variant Classifications

77 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

Likely Pathogenic1

VUS47

Likely Benign6

Benign5

Conflicting1

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	1	0	0	0	1
Likely Pathogenic	1	0	0	0	1
VUS	1	46	0	0	47
Likely Benign	1	3	0	2	6
Benign	0	0	2	3	5
Conflicting	—				1
Total	4	49	2	5	61

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

117 pathogenic / likely-pathogenic (of 144) ClinVar copy-number / structural variants overlap CFAP96 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →