CNOT11
protein-codingCCR4-NOT transcription complex subunit 11, the group of CCR4-NOT transcription complex
Gene summary
Predicted to be involved in nuclear-transcribed mRNA poly(A) tail shortening. Part of CCR4-NOT complex. [provided by Alliance of Genome Resources, Jul 2025]
- C2orf29
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.4 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 CNOT11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017546.5. 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 | 1 | 1 | ||||
| missense | 29 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 33 | 1 | 0 | 34 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060016.3 | 7 | MANE Select | |
| Ensembl | ENSP00000289382.3 | 7 | MANE Select | |
| Ensembl | ENSP00000394203.1 | 3 | Standard | |
| Ensembl | ENSP00000545252.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Gene expression (Transcription)
- Generic Transcription Pathway
- RNA Polymerase II Transcription
- Metabolism of RNA
- TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
Biological Process
- nuclear-transcribed mRNA poly(A) tail shortening
- regulation of translation
- DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
- cell population proliferation
- gene silencing by RNA
Molecular Function
- molecular_function
- protein binding
Cellular Component
- nucleus
- cytosol
- CCR4-NOT complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000289382
- Coding exons
- 7
- Length
- 17515
- Individuals with no LoFs
- 125733
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 125748
- p
- 0.0000596
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.30 | 174 | 283 | 0.615 | 0.0000152 | 3298 |
| Missense (PolyPhen) | 51 | 133.12 | 0.38311 | 1494 | ||
| Synonymous | 0.240 | 108 | 111 | 0.971 | 0.00000591 | 1044 |
| Loss of Function | 3.34 | 4 | 20.2 | 0.198 | 0.00000119 | 221 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.000073 | 0.000070 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Is required for the association of CNOT10 with the CCR4-NOT complex. Seems not to be required for complex deadenylase function.;
Recessive Scores
- pRec
- 0.0908
Intolerance Scores
- RVIS EVS
- -0.36
- RVIS percentile EVS
- 28.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |