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Aliases for C2CD3 Gene

Aliases for C2CD3 Gene

  • C2 Calcium Dependent Domain Containing 3 2 3 5
  • C2 Domain-Containing Protein 3 3
  • OFD14 3

External Ids for C2CD3 Gene

Previous GeneCards Identifiers for C2CD3 Gene

  • GC11M073424
  • GC11M073724
  • GC11M070041

Summaries for C2CD3 Gene

Entrez Gene Summary for C2CD3 Gene

  • This gene encodes a protein that functions as a regulator of centriole elongation. Studies of the orthologous mouse protein show that it promotes centriolar distal appendage assembly and is also required for the recruitment of other ciliogenic proteins, including intraflagellar transport proteins. Mutations in this gene cause orofaciodigital syndrome XIV (OFD14), a ciliopathy resulting in malformations of the oral cavity, face and digits. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Nov 2014]

GeneCards Summary for C2CD3 Gene

C2CD3 (C2 Calcium Dependent Domain Containing 3) is a Protein Coding gene. Diseases associated with C2CD3 include Orofaciodigital Syndrome Xiv and Joubert Syndrome 1. Among its related pathways are Organelle biogenesis and maintenance and Regulation of PLK1 Activity at G2/M Transition.

UniProtKB/Swiss-Prot for C2CD3 Gene

  • Component of the centrioles that acts as a positive regulator of centriole elongation (PubMed:24997988). Promotes assembly of centriolar distal appendage, a structure at the distal end of the mother centriole that acts as an anchor of the cilium, and is required for recruitment of centriolar distal appendages proteins CEP83, SCLT1, CEP89, FBF1 and CEP164. Not required for centriolar satellite integrity or RAB8 activation. Required for primary cilium formation (PubMed:23769972). Required for sonic hedgehog/SHH signaling and for proteolytic processing of GLI3.

Additional gene information for C2CD3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for C2CD3 Gene

Genomics for C2CD3 Gene

GeneHancer (GH) Regulatory Elements for C2CD3 Gene

Promoters and enhancers for C2CD3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J074169 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 658.3 -0.3 -250 3.5 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B NEUROD1 SIN3A YBX1 DMAP1 PPME1 C2CD3 GC11P074171 POLD3 ENSG00000206913 RNF169 P4HA3 PAAF1 RN7SL239P
GH11J073375 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 29.6 +788.4 788413 15 CLOCK DMAP1 IRF4 SLC30A9 E2F8 ZNF416 ZNF143 ZNF548 SP3 GLIS1 RELT ENSG00000206913 C2CD3 ARPC3P4 ARHGEF17 LOC105369379 ENSG00000256448 CLPB P4HA3-AS1 P4HA3
GH11J073597 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 24.5 +573.0 572953 2.3 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 FAM168A POLD3 ENSG00000206913 C2CD3 RELT ARHGEF17 LOC100419713
GH11J074397 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 22.8 -227.2 -227227 2.5 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B ZNF766 PGM2L1 MIR548AL GC11M074397 ENSG00000254631 C2CD3 POLD3 ENSG00000255440 PPME1
GH11J073786 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 20.6 +382.8 382849 3.2 CLOCK FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 MRPL48 POLD3 ENSG00000206913 RNF169 ARPC3P4 RAB6A C2CD3 P4HA3 ENSG00000256034 ENSG00000254837
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around C2CD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the C2CD3 gene promoter:
  • POU2F1a
  • POU2F1
  • SREBP-1c
  • SREBP-1b
  • SREBP-1a
  • HFH-1
  • Gfi-1
  • E2F
  • E2F-1
  • E2F-2

Genomic Locations for C2CD3 Gene

Genomic Locations for C2CD3 Gene
chr11:74,012,714-74,171,210
(GRCh38/hg38)
Size:
158,497 bases
Orientation:
Minus strand
chr11:73,723,763-73,882,255
(GRCh37/hg19)
Size:
158,493 bases
Orientation:
Minus strand

Genomic View for C2CD3 Gene

Genes around C2CD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C2CD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C2CD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C2CD3 Gene

Proteins for C2CD3 Gene

  • Protein details for C2CD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q4AC94-C2CD3_HUMAN
    Recommended name:
    C2 domain-containing protein 3
    Protein Accession:
    Q4AC94
    Secondary Accessions:
    • C9JR55
    • E2QRD1
    • Q2NLE1
    • Q3C1U9
    • Q6ZU92
    • Q8IYM4
    • Q8NB87
    • Q8NDH7
    • Q9Y4M2

    Protein attributes for C2CD3 Gene

    Size:
    2353 amino acids
    Molecular mass:
    260389 Da
    Quaternary structure:
    • Interacts with IFT88, BBS4 and PCM1 (By similarity). Interacts with OFD1; OFD1 may act as a negative regulator of C2CD3. Associates with the BBSome complex.
    SequenceCaution:
    • Sequence=BAC03654.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC86334.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for C2CD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for C2CD3 Gene

Post-translational modifications for C2CD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

No data available for DME Specific Peptides for C2CD3 Gene

Domains & Families for C2CD3 Gene

Gene Families for C2CD3 Gene

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

Protein Domains for C2CD3 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for C2CD3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with C2CD3: view

No data available for UniProtKB/Swiss-Prot for C2CD3 Gene

Function for C2CD3 Gene

Molecular function for C2CD3 Gene

UniProtKB/Swiss-Prot Function:
Component of the centrioles that acts as a positive regulator of centriole elongation (PubMed:24997988). Promotes assembly of centriolar distal appendage, a structure at the distal end of the mother centriole that acts as an anchor of the cilium, and is required for recruitment of centriolar distal appendages proteins CEP83, SCLT1, CEP89, FBF1 and CEP164. Not required for centriolar satellite integrity or RAB8 activation. Required for primary cilium formation (PubMed:23769972). Required for sonic hedgehog/SHH signaling and for proteolytic processing of GLI3.

Gene Ontology (GO) - Molecular Function for C2CD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 24997988
genes like me logo Genes that share ontologies with C2CD3: view
genes like me logo Genes that share phenotypes with C2CD3: view

Human Phenotype Ontology for C2CD3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for C2CD3 Gene

miRTarBase miRNAs that target C2CD3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for C2CD3 Gene

Localization for C2CD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for C2CD3 Gene

Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriole. Note=Localizes to centrioles and procentrioles both in interphase and mitosis. Localizes to centriolar satellites, localization is dependent on PCM1 and dynein-mediated retrograde transport. Also localizes to the distal ends of the mother and daughter centrioles.

Subcellular locations from

COMPARTMENTS
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 C2CD3 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
nucleus 2
plasma membrane 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Microtubule organizing center (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for C2CD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005813 centrosome IDA 21399614
GO:0005814 centriole IEA,IDA 23769972
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with C2CD3: view

Pathways & Interactions for C2CD3 Gene

genes like me logo Genes that share pathways with C2CD3: view

Pathways by source for C2CD3 Gene

Gene Ontology (GO) - Biological Process for C2CD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development IEA --
GO:0001947 heart looping IEA --
GO:0007389 pattern specification process IEA --
GO:0007420 brain development IEA --
GO:0008589 regulation of smoothened signaling pathway IEA --
genes like me logo Genes that share ontologies with C2CD3: view

No data available for SIGNOR curated interactions for C2CD3 Gene

Drugs & Compounds for C2CD3 Gene

No Compound Related Data Available

Transcripts for C2CD3 Gene

Unigene Clusters for C2CD3 Gene

C2 calcium-dependent domain containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for C2CD3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19 ^ 20a · 20b ·
SP1: - - -
SP2: - -
SP3: - - -
SP4: - -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

ExUns: 20c ^ 21a · 21b · 21c ^ 22 ^ 23a · 23b · 23c ^ 24 ^ 25 ^ 26 ^ 27 ^ 28
SP1: -
SP2: - - - - - -
SP3:
SP4: - -
SP5: - -
SP6:
SP7:
SP8:
SP9: - - - -
SP10:

Relevant External Links for C2CD3 Gene

GeneLoc Exon Structure for
C2CD3
ECgene alternative splicing isoforms for
C2CD3

Expression for C2CD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for C2CD3 Gene

Protein differential expression in normal tissues from HIPED for C2CD3 Gene

This gene is overexpressed in Bone (39.9), Bone marrow stromal cell (16.6), and Fetal gut (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for C2CD3 Gene



Protein tissue co-expression partners for C2CD3 Gene

NURSA nuclear receptor signaling pathways regulating expression of C2CD3 Gene:

C2CD3

SOURCE GeneReport for Unigene cluster for C2CD3 Gene:

Hs.694798

Evidence on tissue expression from TISSUES for C2CD3 Gene

  • Nervous system(4.5)
  • Eye(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for C2CD3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • skull
  • tongue
  • tooth
Pelvis:
  • penis
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
General:
  • hair
  • skin
genes like me logo Genes that share expression patterns with C2CD3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for C2CD3 Gene

Orthologs for C2CD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for C2CD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C2CD3 34 33
  • 99.48 (n)
OneToOne
dog
(Canis familiaris)
Mammalia C2CD3 33
  • 87.95 (n)
UCP3 34
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia C2cd3 16 34 33
  • 83.47 (n)
rat
(Rattus norvegicus)
Mammalia C2cd3 33
  • 82.63 (n)
cow
(Bos Taurus)
Mammalia C2CD3 34
  • 70 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia C2CD3 34
  • 51 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia C2CD3 34
  • 46 (a)
OneToOne
chicken
(Gallus gallus)
Aves C2CD3 34 33
  • 60.36 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 55 (a)
OneToMany
-- 34
  • 33 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia c2cd3 33
  • 54.86 (n)
zebrafish
(Danio rerio)
Actinopterygii si:ch211-149e23.1 33
  • 54.13 (n)
C2CD3 34
  • 37 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG32425 34
  • 21 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 40 (a)
OneToMany
-- 34
  • 33 (a)
OneToMany
Species where no ortholog for C2CD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for C2CD3 Gene

ENSEMBL:
Gene Tree for C2CD3 (if available)
TreeFam:
Gene Tree for C2CD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for C2CD3: view image

Paralogs for C2CD3 Gene

(1) SIMAP similar genes for C2CD3 Gene using alignment to 6 proteins:

  • C2CD3_HUMAN
  • F5H0U2_HUMAN
  • H0YFM6_HUMAN
  • H0YG44_HUMAN
  • H7BZB4_HUMAN
  • H7C288_HUMAN
genes like me logo Genes that share paralogs with C2CD3: view

No data available for Paralogs for C2CD3 Gene

Variants for C2CD3 Gene

Sequence variations from dbSNP and Humsavar for C2CD3 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs149366137 pathogenic, Orofaciodigital syndrome xiv 74,084,972(-) T/A splice_acceptor_variant
rs150291837 pathogenic, Joubert syndrome 74,049,431(-) C/T coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs587777653 pathogenic, Orofaciodigital syndrome xiv, Joubert syndrome 74,168,485(-) G/A 5_prime_UTR_variant, coding_sequence_variant, genic_upstream_transcript_variant, non_coding_transcript_variant, stop_gained
rs587777654 pathogenic, Orofaciodigital syndrome xiv, Orofaciodigital syndrome 14 (OFD14) [MIM:615948] 74,095,303(-) A/C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs863225151 pathogenic, Joubert syndrome 74,074,252(-) C/A splice_donor_variant

Structural Variations from Database of Genomic Variants (DGV) for C2CD3 Gene

Variant ID Type Subtype PubMed ID
esv2662605 CNV deletion 23128226
esv2668510 CNV deletion 23128226
esv2744773 CNV deletion 23290073
esv2759837 CNV gain 17122850
esv3328087 CNV insertion 20981092
esv34979 CNV gain 17911159
esv3626828 CNV loss 21293372
esv3626829 CNV loss 21293372
esv3626830 CNV gain 21293372
nsv1069610 CNV deletion 25765185
nsv392 CNV insertion 18451855
nsv525322 CNV gain 19592680

Variation tolerance for C2CD3 Gene

Residual Variation Intolerance Score: 74.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 18.83; 98.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for C2CD3 Gene

Human Gene Mutation Database (HGMD)
C2CD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
C2CD3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C2CD3 Gene

Disorders for C2CD3 Gene

MalaCards: The human disease database

(6) MalaCards diseases for C2CD3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
orofaciodigital syndrome xiv
  • ofd14
joubert syndrome 1
  • jbts1
orofaciodigital syndrome
  • oral-facial-digital syndrome
microcephaly
  • microcephalus
asphyxiating thoracic dystrophy
  • jeune syndrome
- elite association - COSMIC cancer census association via MalaCards
Search C2CD3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

C2CD3_HUMAN
  • Orofaciodigital syndrome 14 (OFD14) [MIM:615948]: A form of orofaciodigital syndrome, a group of heterogeneous disorders characterized by malformations of the oral cavity, face and digits, and associated phenotypic abnormalities that lead to the delineation of various subtypes. OFD14 patients show severe microcephaly, cerebral malformations the molar tooth sign, and intellectual disability in addition to canonical OFDS features. {ECO:0000269 PubMed:24997988}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for C2CD3

genes like me logo Genes that share disorders with C2CD3: view

No data available for Genatlas for C2CD3 Gene

Publications for C2CD3 Gene

  1. The oral-facial-digital syndrome gene C2CD3 encodes a positive regulator of centriole elongation. (PMID: 24997988) Thauvin-Robinet C … Nachury MV (Nature genetics 2014) 3 4 58
  2. Discovering regulators of centriole biogenesis through siRNA-based functional genomics in human cells. (PMID: 23769972) Balestra FR … Gönczy P (Developmental cell 2013) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. (PMID: 29117863) Choudhury NR … Michlewski G (BMC biology 2017) 3 58
  5. Phenotypic and Interaction Profiling of the Human Phosphatases Identifies Diverse Mitotic Regulators. (PMID: 27880917) St-Denis N … Gingras AC (Cell reports 2016) 3 58

Products for C2CD3 Gene

Sources for C2CD3 Gene

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