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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CC2D2A
coiled-coil and C2 domain containing 2A
Chromosome 4 Β· 4p15.32
NCBI Gene: 57545Ensembl: ENSG00000048342.18HGNC: HGNC:29253UniProt: H0Y941
34PubMed Papers
24Diseases
0Drugs
330Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
smoothened signaling pathwaycilium assemblyprotein localization to ciliary transition zonenon-motile cilium assemblyJoubert syndrome 9Joubert syndrome with hepatic defectMeckel syndrome, type 6Meckel syndrome
✦AI Summary

CC2D2A encodes a component of the tectonic-like complex localized at the ciliary transition zone, functioning as a barrier that prevents diffusion of transmembrane proteins between cilia and plasma membranes. The protein is essential for primary cilia formation and sonic hedgehog signaling 1. CC2D2A mutations cause ciliopathies including Joubert syndrome-9, characterized by neurodevelopmental features such as the distinctive 'molar tooth sign' on brain MRI, developmental delay, hypotonia, and oculomotor dysfunction 12. Patient-derived iPSCs from CC2D2A mutation carriers show impaired differentiation into mid-hindbrain and cerebellar granule cells with notable ciliary defects compared to controls 3. CC2D2A-related Joubert syndrome typically presents with motor and language delay, though 74% of patients retain normal intellectual efficiency 2. The gene also associates with focal segmental glomerulosclerosis and nephronophthisis, indicating broader ciliary dysfunction in renal development 4. Additionally, CC2D2A polymorphisms show association with mental retardation susceptibility in Asian populations 5, and recent evidence suggests CC2D2A functions in mechanotransduction pathways relevant to idiopathic pulmonary fibrosis pathogenesis 6. Homozygous truncating variants predict more severe phenotypes 2.

Sources cited
1
CC2D2A essential for primary cilia formation; mutations cause Joubert Syndrome-9 with neurodevelopmental features
PMID: 37107568
2
Largest CC2D2A cohort analysis: developmental delay nearly constant, 74% normal intellectual efficiency, homozygous truncating p.Arg950* linked to severe phenotype
PMID: 36319078
3
CC2D2A patient-derived iPSCs show impaired neuronal differentiation and ciliary defects compared to controls
PMID: 38502237
4
CC2D2A mutations associated with focal segmental glomerulosclerosis and nephronophthisis
PMID: 34435324
5
CC2D2A polymorphisms associated with mental retardation susceptibility in Han Chinese population
PMID: 22023432
6
CC2D2A identified as prognostic gene for idiopathic pulmonary fibrosis, functions in mechanotransduction pathways
PMID: 41408564
Disease Associationsβ“˜24
Joubert syndrome 9Open Targets
0.84Strong
Joubert syndrome with hepatic defectOpen Targets
0.81Strong
Meckel syndrome, type 6Open Targets
0.81Strong
Meckel syndromeOpen Targets
0.74Strong
retinitis pigmentosa 93Open Targets
0.70Strong
Joubert syndromeOpen Targets
0.65Moderate
Joubert syndrome with oculorenal defectOpen Targets
0.62Moderate
ciliopathyOpen Targets
0.57Moderate
genetic disorderOpen Targets
0.54Moderate
Retinal dystrophyOpen Targets
0.52Moderate
Joubert syndrome and related disordersOpen Targets
0.50Moderate
EncephaloceleOpen Targets
0.48Moderate
Polycystic Kidney DiseaseOpen Targets
0.48Moderate
Joubert syndrome 1Open Targets
0.48Moderate
Neurodevelopmental disorderOpen Targets
0.47Moderate
microcephalyOpen Targets
0.44Moderate
clubfootOpen Targets
0.43Moderate
oligohydramniosOpen Targets
0.43Moderate
polydactyly, postaxial, type A1Open Targets
0.43Moderate
Talipes equinovarusOpen Targets
0.43Moderate
COACH syndrome 2UniProt
Joubert syndrome 9UniProt
Meckel syndrome 6UniProt
Retinitis pigmentosa 93UniProt
Pathogenic Variants330
NM_001378615.1(CC2D2A):c.4229G>A (p.Trp1410Ter)Pathogenic
Meckel-Gruber syndrome;Joubert syndrome|Joubert syndrome 9
β˜…β˜…β˜†β˜†2026β†’ Residue 1410
NM_001080522.2(CC2D2A):c.3289delGPathogenic
Meckel syndrome, type 6|Joubert syndrome 9|not provided|Joubert syndrome;Meckel-Gruber syndrome|See cases|Inborn genetic diseases|COACH syndrome 2|CC2D2A-related disorder|Autosomal recessive CC2D2A-related disorders|COACH syndrome 2;Meckel syndrome, type 6;Joubert syndrome 9;Retinitis pigmentosa 93
β˜…β˜…β˜†β˜†2026
NM_001378615.1(CC2D2A):c.1017+1G>APathogenic
Meckel-Gruber syndrome;Joubert syndrome|Joubert syndrome 9|not provided|CC2D2A-related disorder|COACH syndrome 2;Retinitis pigmentosa 93;Meckel syndrome, type 6;Joubert syndrome 9
β˜…β˜…β˜†β˜†2026
NM_001378615.1(CC2D2A):c.4667A>T (p.Asp1556Val)Pathogenic
Joubert syndrome 9|not provided|Joubert syndrome|Meckel-Gruber syndrome;Joubert syndrome|CC2D2A-related disorder|Inborn genetic diseases|COACH syndrome 1|Neurodevelopmental disorder|Joubert syndrome and related disorders|Retinal dystrophy|Retinitis pigmentosa 93;COACH syndrome 2;Joubert syndrome 9;Meckel syndrome, type 6|Ciliopathy
β˜…β˜…β˜†β˜†2026β†’ Residue 1556
NM_001378615.1(CC2D2A):c.4333C>T (p.Arg1445Ter)Pathogenic
not provided|Joubert syndrome 9|Joubert syndrome;Meckel-Gruber syndrome
β˜…β˜…β˜†β˜†2026β†’ Residue 1445
NM_001378615.1(CC2D2A):c.2581G>A (p.Asp861Asn)Pathogenic
Joubert syndrome;Meckel-Gruber syndrome|Joubert syndrome and related disorders|Retinitis pigmentosa 93;Meckel syndrome, type 6;Joubert syndrome 9;COACH syndrome 2
β˜…β˜…β˜†β˜†2026β†’ Residue 861
NM_001378615.1(CC2D2A):c.3341C>T (p.Thr1114Met)Pathogenic
Meckel syndrome, type 6|Joubert syndrome 9|Polydactyly|not provided|Joubert syndrome;Meckel-Gruber syndrome
β˜…β˜…β˜†β˜†2026β†’ Residue 1114
NM_001378615.1(CC2D2A):c.1267C>T (p.Arg423Ter)Pathogenic
Meckel-Gruber syndrome;Joubert syndrome|Joubert syndrome 1|Retinitis pigmentosa 93;Joubert syndrome 9;Meckel syndrome, type 6;COACH syndrome 2|Meckel syndrome, type 6
β˜…β˜…β˜†β˜†2026β†’ Residue 423
NM_001378615.1(CC2D2A):c.394C>T (p.Arg132Ter)Pathogenic
Meckel-Gruber syndrome|not provided|Joubert syndrome;Meckel-Gruber syndrome|Retinal dystrophy|Meckel syndrome, type 6|Joubert syndrome 9;COACH syndrome 2;Retinitis pigmentosa 93;Meckel syndrome, type 6|Joubert syndrome 9
β˜…β˜…β˜†β˜†2026β†’ Residue 132
NM_001378615.1(CC2D2A):c.4179+1delPathogenic
Meckel syndrome, type 6|Joubert syndrome 9|7 conditions|not provided|Joubert syndrome;Meckel-Gruber syndrome|Anencephaly;Renal cyst;Polydactyly|Inborn genetic diseases|Meckel-Gruber syndrome|COACH syndrome 2;Meckel syndrome, type 6;Joubert syndrome 9;Retinitis pigmentosa 93|Nonpapillary renal cell carcinoma|Retinitis pigmentosa 93
β˜…β˜…β˜†β˜†2026
NM_001378615.1(CC2D2A):c.3280del (p.Leu1094fs)Pathogenic
Retinitis pigmentosa 93;COACH syndrome 2;Joubert syndrome 9;Meckel syndrome, type 6|Meckel-Gruber syndrome;Joubert syndrome|Meckel syndrome, type 6
β˜…β˜…β˜†β˜†2026β†’ Residue 1094
NM_001378615.1(CC2D2A):c.3055C>T (p.Arg1019Ter)Pathogenic
Joubert syndrome 9|not provided|Meckel-Gruber syndrome;Joubert syndrome|COACH syndrome 1;Joubert syndrome 9;Meckel syndrome, type 6|CC2D2A-related disorder|Retinitis pigmentosa 93;COACH syndrome 2;Joubert syndrome 9;Meckel syndrome, type 6|Meckel syndrome, type 6|Clear cell carcinoma of kidney
β˜…β˜…β˜†β˜†2026β†’ Residue 1019
NM_001378615.1(CC2D2A):c.4491A>C (p.Gln1497His)Pathogenic
Joubert syndrome 9|Meckel-Gruber syndrome;Joubert syndrome
β˜…β˜…β˜†β˜†2026β†’ Residue 1497
NM_001378615.1(CC2D2A):c.3134T>C (p.Val1045Ala)Pathogenic
Joubert syndrome 9|Meckel-Gruber syndrome;Joubert syndrome|Inborn genetic diseases
β˜…β˜…β˜†β˜†2026β†’ Residue 1045
NM_001378615.1(CC2D2A):c.4465_4468del (p.Asp1489fs)Pathogenic
Joubert syndrome 9|not provided|Joubert syndrome;Meckel-Gruber syndrome|CC2D2A-related disorder|Retinitis pigmentosa 93;COACH syndrome 2;Meckel syndrome, type 6;Joubert syndrome 9|Autosomal recessive CC2D2A-related disorders
β˜…β˜…β˜†β˜†2026β†’ Residue 1489
NM_001378615.1(CC2D2A):c.2710G>T (p.Glu904Ter)Pathogenic
Joubert syndrome 9|Meckel syndrome, type 6
β˜…β˜…β˜†β˜†2025β†’ Residue 904
NM_001378615.1(CC2D2A):c.337-2A>CLikely pathogenic
Meckel-Gruber syndrome;Joubert syndrome|not provided
β˜…β˜…β˜†β˜†2025
NM_001378615.1(CC2D2A):c.2803C>T (p.Arg935Ter)Pathogenic
Meckel-Gruber syndrome;Joubert syndrome|COACH syndrome 2;Meckel syndrome, type 6;Joubert syndrome 9;Retinitis pigmentosa 93|Inborn genetic diseases|CC2D2A-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 935
NM_001378615.1(CC2D2A):c.2683C>T (p.Gln895Ter)Pathogenic
Joubert syndrome 9|COACH syndrome 1;Meckel syndrome, type 6;Joubert syndrome 9|not provided|CC2D2A-related disorder|Joubert syndrome;Meckel-Gruber syndrome|Retinitis pigmentosa 93;COACH syndrome 2;Meckel syndrome, type 6;Joubert syndrome 9
β˜…β˜…β˜†β˜†2025β†’ Residue 895
NM_001378615.1(CC2D2A):c.3325C>T (p.Arg1109Ter)Pathogenic
Joubert syndrome;Meckel-Gruber syndrome|not provided|Neurodevelopmental disorder|Meckel syndrome, type 6;Retinitis pigmentosa 93;Joubert syndrome 9;COACH syndrome 2
β˜…β˜…β˜†β˜†2025β†’ Residue 1109
View on ClinVar β†—
Related Genes
NPHP3Protein interaction100%NPHP1Protein interaction100%AHI1Protein interaction100%OFD1Protein interaction100%CCP110Protein interaction100%TMEM67Protein interaction99%
Tissue Expression6 tissues
Ovary
100%
Heart
90%
Lung
62%
Brain
55%
Liver
38%
Bone Marrow
10%
Gene Interaction Network
Click a node to explore
CC2D2ANPHP3NPHP1AHI1OFD1CCP110TMEM67
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9P2K1
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.85LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.73 [0.62–0.85]
RankingsWhere CC2D2A stands among ~20K protein-coding genes
  • #11,123of 20,598
    Most Researched34
  • #180of 5,498
    Most Pathogenic Variants330 Β· top 5%
  • #7,441of 17,882
    Most Constrained (LOEUF)0.85
Genes detectedCC2D2A
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
PMID: 20301500
1.00
2
Molecular subtyping and prognostic evaluation in idiopathic pulmonary fibrosis: a focus on mechanical-related genes.
PMID: 41408564
J Transl Med Β· 2025
0.90
3
Exome Analysis Reveals Novel Missense and Deletion Variants in the
PMID: 37107568
Genes (Basel) Β· 2023
0.80
4
A girl with a mutation of the ciliary gene CC2D2A presenting with FSGS and nephronophthisis.
PMID: 34435324
CEN Case Rep Β· 2022
0.70
5
Positive association of CC2D1A and CC2D2A gene haplotypes with mental retardation in a Han Chinese population.
PMID: 22023432
DNA Cell Biol Β· 2012
0.60