Joubert syndrome: genes and variants
Joubert syndrome is linked to 3 analyzed proteins (CEP290, SUFU and CHD7). 7 DNA variants are known to cause it; 850 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Also known as: Joubert syndrome 1; Joubert syndrome 10; Joubert syndrome 32; Joubert syndrome 5
Genes linked to Joubert syndrome
CEP290: Centrosomal protein of 290 kDa
It organizes the transition zone of primary and sensory cilia and is essential for ciliary protein trafficking, especially in photoreceptors. Biallelic pathogenic variants cause a broad ciliopathy spectrum including Leber congenital amaurosis, Joubert syndrome, and nephronophthisis-related disease.
5 disease-causing and 838 uncertain variants in CEP290 are linked to Joubert syndrome.
SUFU: Suppressor of fused homolog
It restrains GLI transcription factors and thereby keeps Hedgehog signaling off when pathway activation is absent. Germline loss-of-function variants predispose particularly to infant desmoplastic medulloblastoma and can also cause developmental Hedgehog-pathway phenotypes.
1 disease-causing and 11 uncertain variants in SUFU are linked to Joubert syndrome.
CHD7: ATP-dependent chromatin remodeler CHD7
It regulates chromatin accessibility and developmental gene programs across multiple embryonic tissues. Haploinsufficiency is the major cause of CHARGE syndrome, which can affect the eyes, heart, choanae, growth, genital development, ears, and nervous system.
1 disease-causing and 0 uncertain variants in CHD7 are linked to Joubert syndrome.
Weakly linked (only a few uncertain records): IFT172 and PKD1.
Where Joubert syndrome variants cluster
- CEP290 Self-association (with itself or C-terminus) (positions 1–695): 3 of 5 disease-causing changes, 2.1× more than its size predicts.
Known disease-causing variants in Joubert syndrome
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| CEP290 M1I | 1 | Self-association (with itself or C-terminus) | Disease-causing (★★) |
| CEP290 M1V | 1 | Self-association (with itself or C-terminus) | Disease-causing (★★) |
| CHD7 R2319C | 2319 | Disease-causing (★★) | |
| CEP290 E1568D | 1568 | Coiled coil | Disease-causing (★) |
| CEP290 E1572K | 1572 | Coiled coil | Disease-causing (★) |
| CEP290 I5T | 5 | Self-association (with itself or C-terminus) | Disease-causing (★) |
| SUFU H176R | 176 | Disease-causing |
Same protein, different disease
- CEP290-related ciliopathy is also caused by CEP290 variants; they fall mostly in different places as the Joubert syndrome variants (7 disease-causing).
- CHARGE syndrome is also caused by CHD7 variants; they fall mostly in different places as the Joubert syndrome variants (42 disease-causing).
- CHD7-related CHARGE syndrome is also caused by CHD7 variants; they fall mostly in different places as the Joubert syndrome variants (8 disease-causing).
- Hypogonadotropic hypogonadism 5 with or without anosmia is also caused by CHD7 variants; they fall mostly in different places as the Joubert syndrome variants (7 disease-causing).
Diseases related to Joubert syndrome
- Retinitis pigmentosa, also linked to CEP290
- Leber congenital amaurosis, also linked to CEP290
- Bardet-Biedl syndrome, also linked to CEP290
- CHARGE syndrome, also linked to CHD7
- Gorlin syndrome, also linked to SUFU
- Wiedemann-Steiner syndrome, also linked to CHD7
- Senior-Loken syndrome, also linked to CEP290
- Nephronophthisis, also linked to CEP290
- CHD7-related CHARGE syndrome, also linked to CHD7
- Familial meningioma, also linked to SUFU
- Hypogonadotropic hypogonadism 5 with or without anosmia, also linked to CHD7
- CEP290-related ciliopathy, also linked to CEP290
Frequently asked questions
Which genes are linked to Joubert syndrome?
In CATVariant, Joubert syndrome is linked to 3 analyzed proteins: CEP290 (Centrosomal protein of 290 kDa), SUFU (Suppressor of fused homolog) and CHD7 (ATP-dependent chromatin remodeler CHD7).
How many genetic variants are linked to Joubert syndrome?
903 variants: 7 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 850 are of uncertain significance or have conflicting reports.
Which uncertain variants in Joubert syndrome look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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