CCDC63
protein-codingcoiled-coil domain containing 63
Gene summary
Predicted to be involved in cilium movement; outer dynein arm assembly; and spermatid development. Predicted to be active in axoneme. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~60.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CCDC63 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152591.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 79 | 8 | 87 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 79 | 8 | 0 | 87 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689804.1 | 11 | MANE Select | |
| Ensembl | ENSP00000312399.5 | 11 | MANE Select | |
| RefSeq | NP_001273172.1 | 10 | Standard | |
| RefSeq | NP_001273173.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cilium movement
- spermatid development
- outer dynein arm assembly
Cellular Component
- axoneme
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000308208
- Coding exons
- 11
- Length
- 60767
- Individuals with no LoFs
- 125154
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 592
- Defined
- 125748
- p
- 0.00236
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.235 | 307 | 319 | 0.963 | 0.0000184 | 3754 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0012 | notable |
| Latino/Admixed American | 0.0011 | 0.0010 | notable |
| Ashkenazi Jewish | 0.0018 | 0.0017 | notable |
| East Asian | 0.0012 | 0.0011 | notable |
| Finnish | 0.0044 | 0.0041 | notable |
| European (Non-Finnish) | 0.0034 | 0.0033 | notable |
| South Asian | 0.00066 | 0.00065 | rare |
| Other | 0.0025 | 0.0024 | notable |
dbNSFP Gene Annotations
Source:
- 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
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.143
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |