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Aliases for CC2D2A Gene

Aliases for CC2D2A Gene

  • Coiled-Coil And C2 Domain Containing 2A 2 3 5
  • Coiled-Coil And C2 Domain-Containing Protein 2A 3
  • Meckel Syndrome, Type 6 2
  • KIAA1345 4
  • JBTS9 3
  • MKS6 3

External Ids for CC2D2A Gene

Previous GeneCards Identifiers for CC2D2A Gene

  • GC04P015080
  • GC04P014821

Summaries for CC2D2A Gene

Entrez Gene Summary for CC2D2A Gene

  • This gene encodes a coiled-coil and calcium binding domain protein that appears to play a critical role in cilia formation. Mutations in this gene cause Meckel syndrome type 6, as well as Joubert syndrome type 9. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

GeneCards Summary for CC2D2A Gene

CC2D2A (Coiled-Coil And C2 Domain Containing 2A) is a Protein Coding gene. Diseases associated with CC2D2A include Joubert Syndrome 9 and Meckel Syndrome, Type 6. Among its related pathways are Organelle biogenesis and maintenance and Regulation of PLK1 Activity at G2/M Transition. An important paralog of this gene is CC2D2B.

UniProtKB/Swiss-Prot for CC2D2A Gene

  • Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. Required for ciliogenesis and sonic hedgehog/SHH signaling (By similarity).

Gene Wiki entry for CC2D2A Gene

Additional gene information for CC2D2A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CC2D2A Gene

Genomics for CC2D2A Gene

GeneHancer (GH) Regulatory Elements for CC2D2A Gene

Promoters and enhancers for CC2D2A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J015478 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 650.4 +9.9 9915 2.4 ARNT ARID4B SIN3A DMAP1 ZNF2 ZNF48 YY1 GLIS2 ZNF143 SP3 CC2D2A FBXL5 FAM200B C1QTNF7 ENSG00000273133 PIR61569
GH04J015469 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 650.7 +0.1 78 1.3 SP1 PKNOX1 RFX1 POLR2A ZNF384 CC2D2A LOC101929095 PIR61569
GH04J015339 Promoter 0.5 EPDnew 650.1 -129.9 -129892 0.1 C1QTNF7 CC2D2A GC04P015410 LOC101929095
GH04J014853 Enhancer 0.8 FANTOM5 Ensembl ENCODE 4.8 -616.1 -616079 1.1 JUND GATA3 FOS CC2D2A LINC00504 ENSG00000202449 GC04P014388 GC04P014387
GH04J015484 Enhancer 0.3 FANTOM5 8.5 +14.5 14450 0.4 FAM200B FBXL5 CC2D2A PIR61569
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CC2D2A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CC2D2A gene promoter:
  • IRF-1
  • YY1
  • C/EBPalpha
  • MIF-1
  • Evi-1

Genomic Locations for CC2D2A Gene

Genomic Locations for CC2D2A Gene
132,111 bases
Plus strand
131,692 bases
Plus strand

Genomic View for CC2D2A Gene

Genes around CC2D2A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CC2D2A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CC2D2A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CC2D2A Gene

Proteins for CC2D2A Gene

  • Protein details for CC2D2A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Coiled-coil and C2 domain-containing protein 2A
    Protein Accession:
    Secondary Accessions:
    • A6ND97
    • B3FW08
    • D6RB72
    • E7EP21
    • E9PEV5
    • Q3SYP3
    • Q9H8A7

    Protein attributes for CC2D2A Gene

    1620 amino acids
    Molecular mass:
    186185 Da
    Quaternary structure:
    • Part of the tectonic-like complex (also named B9 complex).
    • Sequence=AAI03711.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA92583.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB14710.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};

    Alternative splice isoforms for CC2D2A Gene


neXtProt entry for CC2D2A Gene

Post-translational modifications for CC2D2A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CC2D2A Gene

Domains & Families for CC2D2A Gene

Gene Families for CC2D2A Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for CC2D2A Gene


Suggested Antigen Peptide Sequences for CC2D2A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CC2D2A: view

No data available for UniProtKB/Swiss-Prot for CC2D2A Gene

Function for CC2D2A Gene

Molecular function for CC2D2A Gene

UniProtKB/Swiss-Prot Function:
Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. Required for ciliogenesis and sonic hedgehog/SHH signaling (By similarity).

Phenotypes From GWAS Catalog for CC2D2A Gene

genes like me logo Genes that share phenotypes with CC2D2A: view

Human Phenotype Ontology for CC2D2A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CC2D2A Gene

MGI Knock Outs for CC2D2A:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for CC2D2A Gene

Localization for CC2D2A Gene

Subcellular locations from UniProtKB/Swiss-Prot for CC2D2A Gene

Cytoplasm. Cytoplasm, cytoskeleton, cilium basal body. Note=Localizes at the transition zone, a region between the basal body and the ciliary axoneme. {ECO:0000250}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CC2D2A gene
Compartment Confidence
cytosol 5
cytoskeleton 4
nucleus 3
mitochondrion 1

Gene Ontology (GO) - Cellular Components for CC2D2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
GO:0005929 cilium IEA --
GO:0035869 ciliary transition zone ISS --
genes like me logo Genes that share ontologies with CC2D2A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CC2D2A Gene

Pathways & Interactions for CC2D2A Gene

genes like me logo Genes that share pathways with CC2D2A: view

Pathways by source for CC2D2A Gene

Interacting Proteins for CC2D2A Gene

Gene Ontology (GO) - Biological Process for CC2D2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001843 neural tube closure IEA --
GO:0007224 smoothened signaling pathway ISS --
GO:0007368 determination of left/right symmetry IEA --
GO:0007507 heart development IEA --
GO:0030030 cell projection organization IEA --
genes like me logo Genes that share ontologies with CC2D2A: view

No data available for SIGNOR curated interactions for CC2D2A Gene

Drugs & Compounds for CC2D2A Gene

No Compound Related Data Available

Transcripts for CC2D2A Gene

Unigene Clusters for CC2D2A Gene

Coiled-coil and C2 domain containing 2A:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CC2D2A Gene

No ASD Table

Relevant External Links for CC2D2A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CC2D2A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CC2D2A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CC2D2A Gene

This gene is overexpressed in Retina (68.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CC2D2A Gene

Protein tissue co-expression partners for CC2D2A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CC2D2A Gene:


SOURCE GeneReport for Unigene cluster for CC2D2A Gene:


mRNA Expression by UniProt/SwissProt for CC2D2A Gene:

Tissue specificity: Strongly expressed in prostate, pancreas, kidney, lung, liver, retina, kidney, fetal brain and fetal kidney. Lower expression in spleen, small intestine, colon, skeletal muscle, ovary, thymus and heart.

Evidence on tissue expression from TISSUES for CC2D2A Gene

  • Nervous system(4.4)
  • Thyroid gland(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CC2D2A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • nose
  • olfactory bulb
  • outer ear
  • salivary gland
  • skull
  • tongue
  • tooth
  • aorta
  • breast
  • clavicle
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
  • abdominal wall
  • adrenal gland
  • biliary tract
  • duodenum
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • spleen
  • stomach
  • anus
  • pelvis
  • penis
  • placenta
  • rectum
  • testicle
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vagina
  • vulva
  • ankle
  • arm
  • digit
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • humerus
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • blood
  • blood vessel
  • coagulation system
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with CC2D2A: view

No data available for mRNA differential expression in normal tissues for CC2D2A Gene

Orthologs for CC2D2A Gene

This gene was present in the common ancestor of animals.

Orthologs for CC2D2A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CC2D2A 34 33
  • 99.61 (n)
(Canis familiaris)
Mammalia CC2D2A 34 33
  • 88.07 (n)
(Bos Taurus)
Mammalia CC2D2A 34 33
  • 84.98 (n)
(Mus musculus)
Mammalia Cc2d2a 16 34 33
  • 84.11 (n)
(Rattus norvegicus)
Mammalia Cc2d2a 33
  • 82.48 (n)
(Ornithorhynchus anatinus)
Mammalia CC2D2A 34
  • 82 (a)
(Monodelphis domestica)
Mammalia CC2D2A 34
  • 75 (a)
(Gallus gallus)
Aves CC2D2A 34 33
  • 72.03 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 79 (a)
-- 34
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cc2d2a 33
  • 65.21 (n)
Str.4091 33
(Danio rerio)
Actinopterygii cc2d2a 34 33
  • 60.7 (n)
wufc03c12 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009813 33
  • 45.29 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG43370 34 33
  • 40.91 (n)
(Caenorhabditis elegans)
Secernentea mks-6 34
  • 14 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 38 (a)
Species where no ortholog for CC2D2A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CC2D2A Gene

Gene Tree for CC2D2A (if available)
Gene Tree for CC2D2A (if available)
Evolutionary constrained regions (ECRs) for CC2D2A: view image

Paralogs for CC2D2A Gene

Paralogs for CC2D2A Gene

(1) SIMAP similar genes for CC2D2A Gene using alignment to 4 proteins:

  • D6R9V3_HUMAN
  • H0Y941_HUMAN
  • L8EC73_HUMAN Pseudogenes for CC2D2A Gene

genes like me logo Genes that share paralogs with CC2D2A: view

Variants for CC2D2A Gene

Sequence variations from dbSNP and Humsavar for CC2D2A Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1134634 benign, likely-benign, not specified, Meckel-Gruber syndrome, Joubert syndrome 15,601,446(+) G/C/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs116198081 likely-benign, uncertain-significance, not specified, Meckel-Gruber syndrome, CC2D2A-Related Disorders, Joubert syndrome 15,514,751(+) A/C/G coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs117667651 likely-benign, uncertain-significance, benign, Joubert syndrome, Meckel-Gruber syndrome, not specified 15,597,398(+) C/A genic_downstream_transcript_variant, intron_variant
rs118204051 pathogenic, Joubert syndrome 9, Joubert syndrome 9 (JBTS9) [MIM:612285] 15,567,752(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs118204052 pathogenic, likely-pathogenic, Joubert syndrome 9, not provided, COACH syndrome (COACHS) [MIM:216360], Joubert syndrome 9 (JBTS9) [MIM:612285] 15,599,614(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for CC2D2A Gene

Variant ID Type Subtype PubMed ID
esv2759227 CNV gain+loss 17122850
nsv428439 CNV gain+loss 18775914
nsv966255 CNV duplication 23825009

Variation tolerance for CC2D2A Gene

Residual Variation Intolerance Score: 97.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.83; 73.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CC2D2A Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CC2D2A Gene

Disorders for CC2D2A Gene

MalaCards: The human disease database

(20) MalaCards diseases for CC2D2A Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
joubert syndrome 9
  • jbts9
meckel syndrome, type 6
  • mks6
coach syndrome
  • cerebellar vermis hypo/aplasia, oligophrenia, congenital ataxia, ocular coloboma, and hepatic fibrosis
  • bifid cranium
meckel syndrome, type 1
  • mks1
- elite association - COSMIC cancer census association via MalaCards


  • Meckel syndrome 6 (MKS6) [MIM:612284]: A disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. {ECO:0000269 PubMed:18513680, ECO:0000269 PubMed:19466712, ECO:0000269 PubMed:24706459}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Joubert syndrome 9 (JBTS9) [MIM:612285]: A disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease. {ECO:0000269 PubMed:18387594, ECO:0000269 PubMed:18950740, ECO:0000269 PubMed:19777577, ECO:0000269 PubMed:22241855, ECO:0000269 PubMed:22246503, ECO:0000269 PubMed:22425360, ECO:0000269 PubMed:23012439, ECO:0000269 PubMed:26477546}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • COACH syndrome (COACHS) [MIM:216360]: A disorder characterized by mental retardation, ataxia due to cerebellar hypoplasia, and hepatic fibrosis. Patients present the molar tooth sign, a midbrain-hindbrain malformation pathognomonic for Joubert syndrome and related disorders. Other features, such as coloboma and renal cysts, may be variable. {ECO:0000269 PubMed:19574260}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for CC2D2A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CC2D2A: view

No data available for Genatlas for CC2D2A Gene

Publications for CC2D2A Gene

  1. Identification of CC2D2A as a Meckel syndrome gene adds an important piece to the ciliopathy puzzle. (PMID: 18513680) Tallila J … Kestilä M (American journal of human genetics 2008) 2 3 4 58
  2. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 58
  3. Genotype-phenotype correlation in CC2D2A-related Joubert syndrome reveals an association with ventriculomegaly and seizures. (PMID: 22241855) Bachmann-Gagescu R … Doherty D (Journal of medical genetics 2012) 3 4 58
  4. Genome-wide association study of conduct disorder symptomatology. (PMID: 20585324) Dick DM … Bierut L (Molecular psychiatry 2011) 3 44 58
  5. Mutations in 3 genes (MKS3, CC2D2A and RPGRIP1L) cause COACH syndrome (Joubert syndrome with congenital hepatic fibrosis). (PMID: 19574260) Doherty D … Glass IA (Journal of medical genetics 2010) 3 4 58

Products for CC2D2A Gene

Sources for CC2D2A Gene

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