CCDC63

coiled-coil domain containing 63

Basic information

Region (hg38): 12:110846768-110907535

Links

ENSG00000173093 ∙ NCBI:160762 ∙ OMIM:617969 ∙ HGNC:26669 ∙ Uniprot:Q8NA47 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC63 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC63 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						0
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	0

Variants in CCDC63

This is a list of pathogenic ClinVar variants found in the CCDC63 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-110853432-G-T		not specified	Uncertain significance (Jan 23, 2023)
12-110853438-C-T		not specified	Uncertain significance (Sep 20, 2023)
12-110853485-G-C		not specified	Uncertain significance (May 09, 2023)
12-110853547-G-A		not specified	Uncertain significance (Mar 01, 2024)
12-110858591-A-C		not specified	Uncertain significance (Nov 15, 2021)
12-110858654-C-T		not specified	Uncertain significance (Jul 13, 2021)
12-110873903-C-T		not specified	Uncertain significance (Nov 12, 2021)
12-110873914-C-T		not specified	Uncertain significance (Aug 02, 2022)
12-110873948-C-A		not specified	Uncertain significance (Dec 20, 2023)
12-110873960-T-C		not specified	Uncertain significance (Jun 06, 2023)
12-110879976-T-A		not specified	Likely benign (Jun 03, 2022)
12-110880035-A-G		not specified	Uncertain significance (Oct 12, 2021)
12-110880045-T-A		not specified	Uncertain significance (Mar 27, 2023)
12-110881144-T-G		not specified	Uncertain significance (Jun 24, 2022)
12-110881145-G-T		not specified	Uncertain significance (Mar 01, 2023)
12-110881152-C-T		not specified	Uncertain significance (Dec 14, 2021)
12-110881153-G-A		not specified	Uncertain significance (May 27, 2022)
12-110884104-C-A		not specified	Uncertain significance (Aug 02, 2021)
12-110884189-C-T		not specified	Uncertain significance (Dec 26, 2023)
12-110884198-C-G		not specified	Uncertain significance (Mar 07, 2023)
12-110884198-C-T		not specified	Uncertain significance (Jun 03, 2022)
12-110884217-G-C		not specified	Uncertain significance (Jul 12, 2022)
12-110893078-C-A		not specified	Uncertain significance (Mar 29, 2024)
12-110898940-T-A		not specified	Uncertain significance (Jan 30, 2024)
12-110898985-G-C		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCDC63	protein_coding	protein_coding	ENST00000308208	11	60767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.27e-19	0.00604	125154	2	592	125748	0.00236

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.235	307	319	0.963	0.0000184	3754
Missense in Polyphen		89	87.366	1.0187		1120
Synonymous	0.692	118	128	0.922	0.00000742	1020
Loss of Function	0.260	29	30.5	0.949	0.00000200	328

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00225	0.00225
Ashkenazi Jewish	0.00177	0.00169
East Asian	0.00115	0.00114
Finnish	0.00444	0.00412
European (Non-Finnish)	0.00343	0.00333
Middle Eastern	0.00115	0.00114
South Asian	0.000657	0.000653
Other	0.00254	0.00245

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in spermiogenesis. Involved in the elongation of flagella and the formation of sperm heads. {ECO:0000250|UniProtKB:Q8CDV6}.

Intolerance Scores

• loftool: 0.961
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.24

Haploinsufficiency Scores

• pHI: 0.0689
• hipred: N
• hipred_score: 0.180
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc63

Gene ontology

• Biological process: cilium movement;spermatid development;outer dynein arm assembly
• Cellular component: axoneme