CCDC12
protein-codingcoiled-coil domain containing 12, the group of Spliceosomal Bact complex|Spliceosomal P complex|Spliceosomal C complex
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 ~65.4 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 CCDC12 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001277074.2. 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 | 2 | 2 | ||||
| missense | 25 | 1 | 26 | |||
| nonsense | 0 | |||||
| start loss | 2 | 2 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 0 | 37 | 1 | 0 | 38 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001264003.1 | 7 | MANE Select | |
| Ensembl | ENSP00000508011.1 | 7 | MANE Select | |
| RefSeq | NP_653317.2 | 7 | Standard | |
| Ensembl | ENSP00000292314.2 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Spliceosome - Homo sapiens (human)
Molecular Function
- protein binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000425441
- Coding exons
- 7
- Length
- 60285
- Individuals with no LoFs
- 125508
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 238
- Defined
- 125748
- p
- 0.000955
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.418 | 89 | 101 | 0.883 | 0.00000555 | 1136 |
| Missense (PolyPhen) | 25 | 32.794 | 0.76234 | 371 | ||
| Synonymous | -0.120 | 43 | 42.0 | 1.02 | 0.00000249 | 336 |
| Loss of Function | 1.91 | 4 | 10.8 | 0.371 | 5.56e-7 | 136 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.016 | 0.013 | notable |
| Latino/Admixed American | 0.00069 | 0.00061 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00013 | 0.00011 | rare |
| Finnish | 0.000052 | 0.000046 | rare |
| European (Non-Finnish) | 0.000050 | 0.000044 | rare |
| South Asian | 0.00016 | 0.00013 | rare |
| Other | 0.00019 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.101
Intolerance Scores
- LoFtool
- 0.197
- RVIS EVS
- 0.1
- RVIS percentile EVS
- 61.49
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Indispensability pred.
- E
- Indispensability score
- 0.583
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |