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    C2CD3 C2 domain containing 3 centriole elongation regulator [ Homo sapiens (human) ]

    Gene ID: 26005, updated on 27-Nov-2024

    Summary

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    Official Symbol
    C2CD3provided by HGNC
    Official Full Name
    C2 domain containing 3 centriole elongation regulatorprovided by HGNC
    Primary source
    HGNC:HGNC:24564
    See related
    Ensembl:ENSG00000168014 MIM:615944; AllianceGenome:HGNC:24564
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    OFD14
    Summary
    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]
    Expression
    Ubiquitous expression in testis (RPKM 5.6), thyroid (RPKM 3.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See C2CD3 in Genome Data Viewer
    Location:
    11q13.4
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (74012718..74171002, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (73942048..74100346, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (73723763..73882047, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 91 member A1 pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:73715060-73716259 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:73719425-73719605 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:73719739-73720378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5249 Neighboring gene uncoupling protein 3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:73747696-73748895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5250 Neighboring gene NANOG hESC enhancer GRCh37_chr11:73808354-73808901 Neighboring gene Sharpr-MPRA regulatory region 9619 Neighboring gene H3K27ac hESC enhancers GRCh37_chr11:73881282-73882205 and GRCh37_chr11:73882206-73883128 Neighboring gene protein phosphatase methylesterase 1 Neighboring gene uncharacterized LOC105369383 Neighboring gene RNA, 5S ribosomal pseudogene 343

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Mutations in human C2CD3 cause skeletal dysplasia and provide new insights into phenotypic and cellular consequences of altered C2CD3 function. Cortés CR, et al. Sci Rep, 2016 Apr 20. PMID 27094867, Free PMC Article
    2. Characterization of three ciliopathy pedigrees expands the phenotype associated with biallelic C2CD3 variants. Boczek NJ, et al. Eur J Hum Genet, 2018 Dec. PMID 30097616, Free PMC Article
    3. SAS-1 is a C2 domain protein critical for centriole integrity in C. elegans. von Tobel L, et al. PLoS Genet, 2014 Nov. PMID 25412110, Free PMC Article
    4. Search for chromosome rearrangements: new approaches toward discovery of novel translocations in head and neck squamous cell carcinoma. Wang VW, et al. Head Neck, 2013 Jun. PMID 22807096
    5. Evolutionary conservation of centriole rotational asymmetry in the human centrosome. Gaudin N, et al. Elife, 2022 Mar 23. PMID 35319462, Free PMC Article

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Evolutionary conservation of centriole rotational asymmetry in the human centrosome.
      Title: Evolutionary conservation of centriole rotational asymmetry in the human centrosome.
    2. CEP120 interacts with C2CD3 and Talpid3 and is required for centriole appendage assembly and ciliogenesis.
      Title: CEP120 interacts with C2CD3 and Talpid3 and is required for centriole appendage assembly and ciliogenesis.
    3. Biallelic C2CD3 variants lead to a broad spectrum of ciliopathy phenotypes.
      Title: Characterization of three ciliopathy pedigrees expands the phenotype associated with biallelic C2CD3 variants.
    4. Talpid3, C2CD3, and OFD1 differentially regulate the assembly of centriole sub-distal appendages, the CEP350/FOP/CEP19 module, centriolar satellites, and actin networks.
      Title: A distal centriolar protein network controls organelle maturation and asymmetry.
    5. Our data provide further evidence that mutations in C2CD3 cause a ciliopathy in humans and expand the previously reported phenotype resulting from C2CD3 dysfunction.
      Title: Mutations in human C2CD3 cause skeletal dysplasia and provide new insights into phenotypic and cellular consequences of altered C2CD3 function.
    6. we uncover that SAS-1 is related to C2CD3, a protein required for complete centriole formation in human cells and affected in a type of oral-facial-digital (OFD) syndrome
      Title: SAS-1 is a C2 domain protein critical for centriole integrity in C. elegans.
    7. Loss of C2CD3 results in short centrioles without subdistal and distal appendages.
      Title: The oral-facial-digital syndrome gene C2CD3 encodes a positive regulator of centriole elongation.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Orofaciodigital syndrome type 14
    MedGen: C4706604 OMIM: 615948 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    integrase gag-pol Analysis of HIV-1 proviral integration sites in antiretroviral treatment patients indicates that C2CD3 gene favors HIV-1 integration for expansion and persistence of infected cells, suggesting HIV-1 IN interacts with C2CD3 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34770, DKFZp586P0123

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in brain development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in centriole elongation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in centriole elongation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in embryonic digit morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heart looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neural plate axis specification IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neural tube development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in non-motile cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization to centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein localization to centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of proteolysis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of smoothened signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in centriolar satellite IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centriolar satellite IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in centriole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in centriole IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ciliary basal body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in microtubule organizing center IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    C2 domain-containing protein 3
    Names
    C2 calcium dependent domain containing 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_041791.1 RefSeqGene

      Range
      5018..163302
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001286577.2 → NP_001273506.1  C2 domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001273506.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AP002392, AP003717
      Consensus CDS
      CCDS66167.1
      UniProtKB/Swiss-Prot
      C9JR55, E2QRD1, Q2NLE1, Q3C1U9, Q4AC94, Q6ZU92, Q8IYM4, Q8NB87, Q8NDH7, Q9Y4M2
      UniProtKB/TrEMBL
      A0A7P0Z475
      Related
      ENSP00000334379.7, ENST00000334126.12
      Conserved Domains (2) summary
      cd00030
      Location:1679 → 1747
      C2; C2 domain
      cd08683
      Location:1199 → 1341
      C2_C2cd3; C2 domain found in C2 calcium-dependent domain containing 3 (C2cd3) proteins

    2. NM_015531.6 → NP_056346.3  C2 domain-containing protein 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks multiple 3' exons and contains an alternate 3' terminal exon, resulting in a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AB231763, AB231764, AK091397, BC110508, BM460060, CD369754, DB068715, DB078025
      Consensus CDS
      CCDS31636.1
      UniProtKB/TrEMBL
      H7BZB4
      Related
      ENSP00000323339.7, ENST00000313663.11
      Conserved Domains (2) summary
      cd00030
      Location:1679 → 1747
      C2; C2 domain
      cd08683
      Location:1199 → 1341
      C2_C2cd3; C2 domain found in C2 calcium-dependent domain containing 3 (C2cd3) proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      74012718..74171002 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      73942048..74100346 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4AC94.4 GenPept UniProtKB/Swiss-Prot:Q4AC94

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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