CCDC110
protein-codingcoiled-coil domain containing 110
Gene summary
Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.6 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 CCDC110 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152775.4. 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 | 104 | 6 | 110 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 105 | 6 | 0 | 111 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689988.1 | 7 | MANE Select | |
| Ensembl | ENSP00000306776.3 | 7 | MANE Select | |
| RefSeq | NP_001138883.1 | 6 | Standard | |
| Ensembl | ENSP00000377172.3 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
Cellular Component
- nucleus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000307588
- Coding exons
- 7
- Length
- 26578
- Individuals with no LoFs
- 125329
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 419
- Defined
- 125748
- p
- 0.00167
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.623 | 365 | 400 | 0.912 | 0.0000185 | 5591 |
| Missense (PolyPhen) | 92 | 101.52 | 0.90618 | 1658 | ||
| Synonymous | 0.279 | 135 | 139 | 0.970 | 0.00000698 | 1397 |
| Loss of Function | 0.474 | 30 | 32.9 | 0.911 | 0.00000162 | 473 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0016 | 0.0015 | notable |
| Latino/Admixed American | 0.0059 | 0.0058 | notable |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00068 | 0.00065 | rare |
| Finnish | 0.000095 | 0.000092 | rare |
| European (Non-Finnish) | 0.0013 | 0.0012 | notable |
| South Asian | 0.0010 | 0.00095 | rare |
| Other | 0.0020 | 0.0020 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0833
Intolerance Scores
- LoFtool
- 0.996
- RVIS EVS
- 3
- RVIS percentile EVS
- 99.22
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0523
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |