CCDC78 (coiled-coil domain containing 78)

Gene

• Entrez ID: 124093
• Gene name: Coiled-coil domain containing 78
• Gene symbol: CCDC78
• Synonyms (NCBI Gene): C16orf25, CNM4, JFP10, hsCCDC78
• Chromosome: 16
• Chromosome location: 16p13.3
• Summary: The product of this gene contains two coiled-coil domains. The function of this gene is currently unknown. [provided by RefSeq, Sep 2012]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs148595483	G>A,T	Conflicting-interpretations-of-pathogenicity	Missense variant, genic upstream transcript variant, synonymous variant, non coding transcript variant, intron variant, upstream transcript variant, coding sequence variant
rs200865845	G>A	Likely-pathogenic	Missense variant, upstream transcript variant, genic upstream transcript variant, coding sequence variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT869851	hsa-miR-1202	CLIP-seq
MIRT869852	hsa-miR-3130-3p	CLIP-seq
MIRT869853	hsa-miR-3180-5p	CLIP-seq
MIRT869854	hsa-miR-3194-5p	CLIP-seq
MIRT869855	hsa-miR-331-3p	CLIP-seq
MIRT869856	hsa-miR-3943	CLIP-seq
MIRT869857	hsa-miR-3972	CLIP-seq
MIRT869858	hsa-miR-4286	CLIP-seq
MIRT869859	hsa-miR-4685-5p	CLIP-seq
MIRT869860	hsa-miR-4722-3p	CLIP-seq
MIRT869861	hsa-miR-615-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003009	Process	Skeletal muscle contraction	IMP	22818856
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005814	Component	Centriole	IDA	24075808
GO:0005814	Component	Centriole	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0016020	Component	Membrane	IEA
GO:0016529	Component	Sarcoplasmic reticulum	IDA	22818856
GO:0016529	Component	Sarcoplasmic reticulum	IEA
GO:0030030	Process	Cell projection organization	IEA
GO:0042383	Component	Sarcolemma	IDA	22818856
GO:0042383	Component	Sarcolemma	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	22818856
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0098535	Process	De novo centriole assembly involved in multi-ciliated epithelial cell differentiation	IDA	24075808
GO:0098536	Component	Deuterosome	IDA	24075808

Other IDs

• MIM: 614666
• HGNC: 14153
• e!Ensembl: ENSG00000162004

Protein

• UniProt ID: A2IDD5
• Protein name: Coiled-coil domain-containing protein 78 (hsCCDC78)
• Protein function: Component of the deuterosome, a structure that promotes de novo centriole amplification in multiciliated cells that can generate more than 100 centrioles. Deuterosome-mediated centriole amplification occurs in terminally differentiated multicili
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF14739	DUF4472	54 → 165	Domain of unknown function (DUF4472)	Family

• Tissue specificity: TISSUE SPECIFICITY: Expressed primarily in skeletal muscle. {ECO:0000269|PubMed:22818856}.
• Sequence:

  MEHAATTGPRPGPPSRRVENVVLRAKDWLPGAPGGTAVWATSLEAEVPPDLALNKEQQLQ
  ISKELVDIQITTHHLHEQHEAEIFQLKSEILRLESRVLELELRGDGTSQGCAVPVESDPR
  HPRAAAQELRHKAQVPGHSDDHRFQVQPKNTMNPENEQHRLGSGLQGEVKWALEHQEARQ
  QALVTRVATLGRQLQGAREEARAAGQRLATQAVVLCSCQGQLRQAEAENARLQLQLKKLK
  DEYVLRLQHCAWQAVEHADGAGQAPATTALRTFLEATLEDIRAAHRSREQQLARAARSYH
  KRLVDLSRRHEELLVAYRAPGNPQAIFDIASLDLEPLPVPLVTDFSHREDQHGGPGALLS
  SPKKRPGGASQGGTSEPQGLDAASWAQIHQKLRDFSRSTQSWNGSGHSCWSGPRWLKSNF
  LSYRSTWTSTWAGTSTKS

• Sequence length: 438

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CCDC78-related disorder	Likely benign; Benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Centronuclear myopathy	Conflicting classifications of pathogenicity	ClinVar ClinGen, Disgenet, GWAS catalog ClinGen, Disgenet, GWAS catalog	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Cervical cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital myopathy with internal nuclei and atypical cores	Uncertain significance; Conflicting classifications of pathogenicity; Likely benign; Benign	ClinVar CTD, ClinVar, Disgenet, Orphanet CTD, ClinVar, Disgenet, Orphanet CTD, ClinVar, Disgenet, Orphanet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CONGENITAL STRUCTURAL MYOPATHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Autosomal Dominant Myotubular Myopathy	Centronuclear Myopathy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Autosomal Recessive Centronuclear Myopathy	Centronuclear Myopathy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Centronuclear myopathy	Centronuclear Myopathy	CLINGEN_DG	22818856, 25635128		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Centronuclear myopathy	Centronuclear Myopathy	CTD_human_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	31612869	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Fiber Type Disproportion	Congenital myopathy with fiber type disproportion	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Congenital myopathy (disorder)	Congenital myopathy	BEFREE	22818856		★☆☆☆☆ Found in Text Mining only
Congenital myopathy with internal nuclei and atypical cores	Congenital Myopathy With Internal Nuclei And Atypical Cores	Orphanet			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Congenital Structural Myopathy	Congenital Structural Myopathy	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Impaired cognition	Impaired Cognition	HPO_DG			★☆☆☆☆ Found in Text Mining only
Myopathy	Myopathy	BEFREE	22818856		★☆☆☆☆ Found in Text Mining only
Myopathy, Centronuclear, 1	Myopathy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
MYOPATHY, CENTRONUCLEAR, 4	Myopathy	GENOMICS_ENGLAND_DG	22818856		★☆☆☆☆ Found in Text Mining only
MYOPATHY, CENTRONUCLEAR, 4	Myopathy	ORPHANET_DG	22818856		★☆☆☆☆ Found in Text Mining only
Myopathy, Centronuclear, Autosomal Dominant	Myopathy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Tubular Aggregate Myopathy	Tubular Aggregate Myopathy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
X-linked centronuclear myopathy	Centronuclear Myopathy, X-Linked	CTD_human_DG			★☆☆☆☆ Found in Text Mining only