CCDC78

coiled-coil domain containing 78

Basic information

Region (hg38): 16:722582-726954

Previous symbols: [ "C16orf25" ]

Links

ENSG00000162004 ∙ NCBI:124093 ∙ OMIM:614666 ∙ HGNC:14153 ∙ Uniprot:A2IDD5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital myopathy with internal nuclei and atypical cores (Limited), mode of inheritance: AD
• congenital myopathy with internal nuclei and atypical cores (Supportive), mode of inheritance: AD
• centronuclear myopathy (Limited), mode of inheritance: AD
• congenital myopathy with internal nuclei and atypical cores (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myopathy, centronuclear, 4	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal	22818856

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC78 gene.

• Congenital_myopathy_with_internal_nuclei_and_atypical_cores (549 variants)
• Inborn_genetic_diseases (94 variants)
• not_provided (63 variants)
• not_specified (30 variants)
• CCDC78-related_disorder (20 variants)
• Centronuclear_myopathy (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC78 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001378030.1. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			15	105	5	125
missense			226	60	2	288
nonsense			15	3		18
start loss			1			1
frameshift			13			13
splice donor/acceptor (+/-2bp)			14	3		17
Total	0	0	284	171	7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC78	protein_coding	protein_coding	ENST00000293889	14	4373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.97e-31	4.96e-7	124787	0	682	125469	0.00272

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.860	313	273	1.15	0.0000173	2779
Missense in Polyphen		81	72.368	1.1193		852
Synonymous	-0.360	115	110	1.04	0.00000672	897
Loss of Function	-1.94	40	28.8	1.39	0.00000159	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00835	0.00812
Ashkenazi Jewish	0.00140	0.00139
East Asian	0.00149	0.00131
Finnish	0.00944	0.00812
European (Non-Finnish)	0.00213	0.00210
Middle Eastern	0.00149	0.00131
South Asian	0.000430	0.000425
Other	0.00282	0.00278

dbNSFP

Source: dbNSFP

• Function: 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 multiciliated cells (G1/0) and not in S phase. Essential for centriole amplification and is required for CEP152 localization to the deuterosome. {ECO:0000269|PubMed:24075808}.

Intolerance Scores

• loftool: 0.960
• rvis_EVS: 1.42
• rvis_percentile_EVS: 94.97

Haploinsufficiency Scores

• pHI: 0.0832
• hipred: N
• hipred_score: 0.146
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0620

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ccdc78

Zebrafish Information Network

• Gene name: ccdc78
• Affected structure: skeletal muscle cell
• Phenotype tag: abnormal
• Phenotype quality: has extra parts of type

Gene ontology

• Biological process: skeletal muscle contraction;cell projection organization;de novo centriole assembly involved in multi-ciliated epithelial cell differentiation
• Cellular component: centriole;sarcoplasmic reticulum;sarcolemma;perinuclear region of cytoplasm;deuterosome