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    CCDC78 coiled-coil domain containing 78 [ Homo sapiens (human) ]

    Gene ID: 124093, updated on 9-Dec-2024

    Summary

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    Official Symbol
    CCDC78provided by HGNC
    Official Full Name
    coiled-coil domain containing 78provided by HGNC
    Primary source
    HGNC:HGNC:14153
    See related
    Ensembl:ENSG00000162004 MIM:614666; AllianceGenome:HGNC:14153
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CNM4; JFP10; C16orf25; hsCCDC78
    Summary
    Involved in de novo centriole assembly involved in multi-ciliated epithelial cell differentiation and skeletal muscle contraction. Located in several cellular components, including centriole; deuterosome; and sarcolemma. Implicated in centronuclear myopathy 4. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in lung (RPKM 2.8), spleen (RPKM 1.3) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CCDC78 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (722582..726880, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (726756..731054, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (772582..776880, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10214 Neighboring gene F-box and leucine rich repeat protein 16 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:750057-750886 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr16:756390-757006 and GRCh37_chr16:757007-757622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6944 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:764134-764732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6945 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:765331-765928 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:765929-766526 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:766527-767124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:769722-770429 Neighboring gene meteorin, glial cell differentiation regulator Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:770430-771136 Neighboring gene adenine nucleotide translocase lysine methyltransferase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6953 Neighboring gene hydroxyacylglutathione hydrolase like Neighboring gene cytosolic iron-sulfur assembly component 3 Neighboring gene Sharpr-MPRA regulatory region 977 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:790544-791139

    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. CCDC78: Unveiling the Function of a Novel Gene Associated with Hereditary Myopathy. Lopergolo D, et al. Cells, 2024 Sep 8. PMID 39273074, Free PMC Article
    2. The Influence of a Genetic Variant in CCDC78 on LMNA-Associated Skeletal Muscle Disease. Mohar NP, et al. Int J Mol Sci, 2024 Apr 30. PMID 38732148, Free PMC Article
    3. Dominant mutation of CCDC78 in a unique congenital myopathy with prominent internal nuclei and atypical cores. Majczenko K, et al. Am J Hum Genet, 2012 Aug 10. PMID 22818856, Free PMC Article
    4. Deuterosome-mediated centriole biogenesis. Klos Dehring DA, et al. Dev Cell, 2013 Oct 14. PMID 24075808, Free PMC Article
    5. Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16. Daniels RJ, et al. Hum Mol Genet, 2001 Feb 15. PMID 11157797

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CCDC78: Unveiling the Function of a Novel Gene Associated with Hereditary Myopathy.
      Title: CCDC78: Unveiling the Function of a Novel Gene Associated with Hereditary Myopathy.
    2. The Influence of a Genetic Variant in CCDC78 on LMNA-Associated Skeletal Muscle Disease.
      Title: The Influence of a Genetic Variant in CCDC78 on LMNA-Associated Skeletal Muscle Disease.
    3. Dominant mutation of CCDC78 in a unique congenital myopathy with prominent internal nuclei and atypical cores.
      Title: Dominant mutation of CCDC78 in a unique congenital myopathy with prominent internal nuclei and atypical cores.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    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
    Congenital myopathy with internal nuclei and atypical cores
    MedGen: C4707232 OMIM: 614807 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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • FLJ34512

    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 cell projection organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in de novo centriole assembly involved in multi-ciliated epithelial cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in skeletal muscle contraction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in centriole IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in deuterosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in sarcolemma IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in sarcoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 78

    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_032932.1 RefSeqGene

      Range
      5031..8892
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_705

    mRNA and Protein(s)

    1. NM_001031737.3 → NP_001026907.2  coiled-coil domain-containing protein 78 isoform 1

      See identical proteins and their annotated locations for NP_001026907.2

      Status: VALIDATED

      Source sequence(s)
      BC042110, Z98258
      Consensus CDS
      CCDS32353.1
      UniProtKB/Swiss-Prot
      A2IDD5, B4DNY4, B4E1U6, Q05BY7, Q05CA0, Q6T2V5, Q6ZR33, Q8IUR3, Q8NAY7, Q96S12
      Related
      ENSP00000293889.6, ENST00000293889.10
      Conserved Domains (1) summary
      pfam14739
      Location:56 → 164
      DUF4472; Domain of unknown function (DUF4472)

    2. NM_001378030.1 → NP_001364959.1  coiled-coil domain-containing protein 78 isoform 3

      Status: VALIDATED

      Source sequence(s)
      Z98258
      Consensus CDS
      CCDS92076.1
      UniProtKB/TrEMBL
      H3BLT8
      Related
      ENSP00000316851.5, ENST00000345165.10
      Conserved Domains (2) summary
      TIGR02168
      Location:80 → 313
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam14739
      Location:56 → 164
      DUF4472; Domain of unknown function (DUF4472)

    3. NM_001378031.1 → NP_001364960.1  coiled-coil domain-containing protein 78 isoform 4

      Status: VALIDATED

      Source sequence(s)
      Z98258
      Conserved Domains (2) summary
      TIGR02168
      Location:80 → 384
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam14739
      Location:56 → 164
      DUF4472; Domain of unknown function (DUF4472)

    4. NM_001378033.1 → NP_001364962.1  coiled-coil domain-containing protein 78 isoform 5

      Status: VALIDATED

      Source sequence(s)
      Z98258

    RNA

    1. NR_165382.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      Z98258

    2. NR_165383.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      Z98258

    3. NR_165384.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      Z98258
      Related
      ENST00000466708.5

    4. NR_165385.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      Z98258

    5. NR_165386.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      Z98258
      Related
      ENST00000463539.5

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      722582..726880 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433606.1 → XP_047289562.1  coiled-coil domain-containing protein 78 isoform X22

    2. XM_047433605.1 → XP_047289561.1  coiled-coil domain-containing protein 78 isoform X21

    3. XM_047433604.1 → XP_047289560.1  coiled-coil domain-containing protein 78 isoform X19

    4. XM_047433603.1 → XP_047289559.1  coiled-coil domain-containing protein 78 isoform X19

    5. XM_011522370.2 → XP_011520672.1  coiled-coil domain-containing protein 78 isoform X20

      Conserved Domains (1) summary
      pfam14739
      Location:56 → 90
      DUF4472; Domain of unknown function (DUF4472)

    6. XM_006720843.5 → XP_006720906.1  coiled-coil domain-containing protein 78 isoform X18

      Related
      ENST00000485091.5
      Conserved Domains (1) summary
      pfam14739
      Location:56 → 164
      DUF4472; Domain of unknown function (DUF4472)

    7. XM_011522369.2 → XP_011520671.1  coiled-coil domain-containing protein 78 isoform X17

      Conserved Domains (1) summary
      pfam14739
      Location:56 → 164
      DUF4472; Domain of unknown function (DUF4472)

    8. XM_011522366.2 → XP_011520668.1  coiled-coil domain-containing protein 78 isoform X12

      Conserved Domains (1) summary
      pfam14739
      Location:56 → 235
      DUF4472; Domain of unknown function (DUF4472)

    9. XM_011522368.2 → XP_011520670.1  coiled-coil domain-containing protein 78 isoform X16

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 251
      DUF4472; Domain of unknown function (DUF4472)

    10. XM_011522367.2 → XP_011520669.1  coiled-coil domain-containing protein 78 isoform X15

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 164
      DUF4472; Domain of unknown function (DUF4472)

    11. XM_047433602.1 → XP_047289558.1  coiled-coil domain-containing protein 78 isoform X14

    12. XM_006720838.2 → XP_006720901.1  coiled-coil domain-containing protein 78 isoform X13

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 238
      DUF4472; Domain of unknown function (DUF4472)

    13. XM_011522365.2 → XP_011520667.1  coiled-coil domain-containing protein 78 isoform X11

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 238
      DUF4472; Domain of unknown function (DUF4472)

    14. XM_011522360.2 → XP_011520662.1  coiled-coil domain-containing protein 78 isoform X5

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 298
      DUF4472; Domain of unknown function (DUF4472)

    15. XM_011522359.2 → XP_011520661.1  coiled-coil domain-containing protein 78 isoform X4

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 298
      DUF4472; Domain of unknown function (DUF4472)

    16. XM_011522357.2 → XP_011520659.1  coiled-coil domain-containing protein 78 isoform X2

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 309
      DUF4472; Domain of unknown function (DUF4472)

    17. XM_011522364.2 → XP_011520666.1  coiled-coil domain-containing protein 78 isoform X10

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 309
      DUF4472; Domain of unknown function (DUF4472)

    18. XM_011522363.2 → XP_011520665.1  coiled-coil domain-containing protein 78 isoform X9

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 309
      DUF4472; Domain of unknown function (DUF4472)

    19. XM_011522362.2 → XP_011520664.1  coiled-coil domain-containing protein 78 isoform X8

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 309
      DUF4472; Domain of unknown function (DUF4472)

    20. XM_017022929.2 → XP_016878418.1  coiled-coil domain-containing protein 78 isoform X7

    21. XM_011522361.2 → XP_011520663.1  coiled-coil domain-containing protein 78 isoform X6

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 309
      DUF4472; Domain of unknown function (DUF4472)

    22. XM_011522358.3 → XP_011520660.1  coiled-coil domain-containing protein 78 isoform X3

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 309
      DUF4472; Domain of unknown function (DUF4472)

    23. XM_011522356.2 → XP_011520658.1  coiled-coil domain-containing protein 78 isoform X1

      Conserved Domains (1) summary
      pfam14739
      Location:130 → 309
      DUF4472; Domain of unknown function (DUF4472)

    24. XM_047433607.1 → XP_047289563.1  coiled-coil domain-containing protein 78 isoform X23

      Related
      ENST00000460023.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      726756..731054 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379584.1 → XP_054235559.1  coiled-coil domain-containing protein 78 isoform X22

    2. XM_054379583.1 → XP_054235558.1  coiled-coil domain-containing protein 78 isoform X21

    3. XM_054379582.1 → XP_054235557.1  coiled-coil domain-containing protein 78 isoform X19

    4. XM_054379581.1 → XP_054235556.1  coiled-coil domain-containing protein 78 isoform X20

    5. XM_054379580.1 → XP_054235555.1  coiled-coil domain-containing protein 78 isoform X18

    6. XM_054379579.1 → XP_054235554.1  coiled-coil domain-containing protein 78 isoform X17

    7. XM_054379574.1 → XP_054235549.1  coiled-coil domain-containing protein 78 isoform X12

    8. XM_054379578.1 → XP_054235553.1  coiled-coil domain-containing protein 78 isoform X16

    9. XM_054379577.1 → XP_054235552.1  coiled-coil domain-containing protein 78 isoform X15

    10. XM_054379576.1 → XP_054235551.1  coiled-coil domain-containing protein 78 isoform X14

    11. XM_054379575.1 → XP_054235550.1  coiled-coil domain-containing protein 78 isoform X13

    12. XM_054379573.1 → XP_054235548.1  coiled-coil domain-containing protein 78 isoform X11

    13. XM_054379567.1 → XP_054235542.1  coiled-coil domain-containing protein 78 isoform X5

    14. XM_054379566.1 → XP_054235541.1  coiled-coil domain-containing protein 78 isoform X4

    15. XM_054379564.1 → XP_054235539.1  coiled-coil domain-containing protein 78 isoform X2

    16. XM_054379572.1 → XP_054235547.1  coiled-coil domain-containing protein 78 isoform X10

    17. XM_054379571.1 → XP_054235546.1  coiled-coil domain-containing protein 78 isoform X9

    18. XM_054379570.1 → XP_054235545.1  coiled-coil domain-containing protein 78 isoform X8

    19. XM_054379569.1 → XP_054235544.1  coiled-coil domain-containing protein 78 isoform X7

    20. XM_054379568.1 → XP_054235543.1  coiled-coil domain-containing protein 78 isoform X6

    21. XM_054379565.1 → XP_054235540.1  coiled-coil domain-containing protein 78 isoform X3

    22. XM_054379563.1 → XP_054235538.1  coiled-coil domain-containing protein 78 isoform X1

    23. XM_054379585.1 → XP_054235560.1  coiled-coil domain-containing protein 78 isoform X23

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_173476.2: Suppressed sequence

      Description
      NM_173476.2: This RefSeq was suppressed because insufficient evidence exists for the exon combination of this transcript variant, which was based on AK128538.1.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2IDD5.1 GenPept UniProtKB/Swiss-Prot:A2IDD5

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