CEP290

Chr 12AR

centrosomal protein 290

Also known as: 3H11Ag, BBS14, CT87, JBTS5, LCA10, MKS4, NPHP6, POC3

This protein is essential for cilia formation and function, regulating early ciliogenesis steps, centrosomal recruitment of ciliary proteins, and ciliary membrane composition. Autosomal recessive mutations cause a spectrum of ciliopathies including Joubert syndrome, Leber congenital amaurosis, Meckel syndrome, Senior-Loken syndrome, and Bardet-Biedl syndrome. The pathogenic mechanism involves disrupted ciliary assembly and transport processes, particularly affecting retinal photoreceptors and other ciliated tissues.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.985 OMIM phenotypes
Clinical SummaryCEP290
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Gene-Disease Validity (ClinGen)
CEP290-related ciliopathy · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Clinical Trials
4 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
0.98LOEUF
pLI 0.000
Z-score 1.69
OE 0.84 (0.710.98)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.47Z-score
OE missense 0.96 (0.911.01)
949 obs / 991.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.84 (0.710.98)
00.351.4
Missense OE0.96 (0.911.01)
00.61.4
Synonymous OE0.99
01.21.6
LoF obs/exp: 104 / 124.3Missense obs/exp: 949 / 991.0Syn Z: 0.13
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveCEP290-related Joubert syndromeLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6454th %ile
GOF
0.5758th %ile
LOF
0.4332th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

CEP290 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗