CCDC78

coiled-coil domain containing 78

Basic information

Region (hg38): 16:722581-726954

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 (Strong), mode of inheritance: AD
• congenital myopathy with internal nuclei and atypical cores (Supportive), mode of inheritance: AD
• congenital myopathy with internal nuclei and atypical cores (Limited), mode of inheritance: AD
• centronuclear myopathy (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 (470 variants)
• not provided (67 variants)
• not specified (28 variants)
• Inborn genetic diseases (24 variants)
• CCDC78-related condition (4 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	81	4	89
missense			191	36	2	229
nonsense			12	3		15
start loss			1			1
frameshift			11			11
inframe indel			3			3
splice donor/acceptor (+/-2bp)			11	1		12
splice region			16	19	1	36
non coding			6	69	25	100
Total	0	0	239	190	31

Variants in CCDC78

This is a list of pathogenic ClinVar variants found in the CCDC78 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-722600-A-C			Benign (Aug 30, 2018)
16-722645-A-AGCTCTGCTCT			Likely benign (Dec 19, 2019)
16-722762-C-T			Likely benign (Sep 01, 2023)
16-722768-C-T		not specified	Likely benign (-)
16-722772-A-G		CCDC78-related disorder	Uncertain significance (Mar 09, 2023)
16-722779-C-T		Congenital myopathy with internal nuclei and atypical cores	Likely benign (Apr 06, 2023)
16-722780-G-A		Congenital myopathy with internal nuclei and atypical cores	Uncertain significance (Jan 02, 2024)
16-722780-G-C		Congenital myopathy with internal nuclei and atypical cores	Uncertain significance (Jun 09, 2022)
16-722783-C-T		Congenital myopathy with internal nuclei and atypical cores	Uncertain significance (Jan 13, 2023)
16-722784-T-C		Congenital myopathy with internal nuclei and atypical cores	Uncertain significance (Jun 04, 2023)
16-722790-C-G		Congenital myopathy with internal nuclei and atypical cores	Uncertain significance (Jun 20, 2022)
16-722797-G-T		Congenital myopathy with internal nuclei and atypical cores	Benign/Likely benign (Jan 05, 2024)
16-722799-G-A		Congenital myopathy with internal nuclei and atypical cores	Likely benign (Sep 21, 2019)
16-722808-C-A		Congenital myopathy with internal nuclei and atypical cores	Likely benign (May 19, 2021)
16-722808-C-T		Congenital myopathy with internal nuclei and atypical cores	Likely benign (Mar 12, 2023)
16-722842-T-C		Congenital myopathy with internal nuclei and atypical cores	Benign (Jul 14, 2021)
16-722848-C-T			Benign (Jul 27, 2018)
16-722867-C-T			Likely benign (Oct 27, 2018)
16-722908-C-T		Congenital myopathy with internal nuclei and atypical cores	Likely benign (Jun 28, 2023)
16-722912-C-T		Congenital myopathy with internal nuclei and atypical cores	Likely benign (Nov 07, 2023)
16-722924-G-T		Congenital myopathy with internal nuclei and atypical cores	Uncertain significance (Aug 21, 2020)
16-722925-C-T		Congenital myopathy with internal nuclei and atypical cores	Uncertain significance (Nov 02, 2022)
16-722927-C-G		Inborn genetic diseases	Uncertain significance (Dec 15, 2023)
16-722931-T-C		Congenital myopathy with internal nuclei and atypical cores	Uncertain significance (Feb 27, 2023)
16-722935-G-A		Congenital myopathy with internal nuclei and atypical cores	Likely benign (Aug 02, 2022)

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