CNOT6
CCR4-NOT transcription complex subunit 6, the group of CCR4-NOT transcription complex
Basic information
Region (hg38): 5:180494379-180578358
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNOT6 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 | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 0 | 0 |
Variants in CNOT6
This is a list of pathogenic ClinVar variants found in the CNOT6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-180529281-C-T | not specified | Uncertain significance (Jan 25, 2023) | ||
| 5-180529310-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 5-180529341-A-G | not specified | Uncertain significance (Jun 04, 2024) | ||
| 5-180529370-G-A | not specified | Uncertain significance (Dec 11, 2023) | ||
| 5-180549940-G-A | not specified | Uncertain significance (Dec 02, 2022) | ||
| 5-180550078-G-A | not specified | Uncertain significance (Sep 01, 2021) | ||
| 5-180553388-A-T | not specified | Uncertain significance (Jul 08, 2022) | ||
| 5-180553439-A-G | not specified | Uncertain significance (Jul 20, 2022) | ||
| 5-180564741-C-T | not specified | Uncertain significance (Jul 30, 2023) | ||
| 5-180565879-T-C | not specified | Uncertain significance (Jun 07, 2023) | ||
| 5-180565882-G-A | not specified | Uncertain significance (Dec 11, 2023) | ||
| 5-180567184-A-G | not specified | Uncertain significance (Jun 10, 2024) | ||
| 5-180567200-G-A | not specified | Uncertain significance (Dec 01, 2023) | ||
| 5-180567223-A-G | not specified | Uncertain significance (Oct 17, 2023) | ||
| 5-180569124-C-T | not specified | Uncertain significance (Jan 26, 2023) | ||
| 5-180569256-C-T | not specified | Uncertain significance (May 17, 2023) | ||
| 5-180569281-G-A | not specified | Uncertain significance (Dec 28, 2023) | ||
| 5-180571326-A-G | not specified | Uncertain significance (May 09, 2024) | ||
| 5-180571349-G-A | not specified | Uncertain significance (Jan 19, 2022) | ||
| 5-180571391-A-G | not specified | Uncertain significance (Dec 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CNOT6 | protein_coding | protein_coding | ENST00000393356 | 11 | 83994 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0195 | 0.980 | 125737 | 0 | 10 | 125747 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.38 | 184 | 300 | 0.614 | 0.0000152 | 3660 |
| Missense in Polyphen | 29 | 77.562 | 0.37389 | 972 | ||
| Synonymous | 0.0120 | 112 | 112 | 0.999 | 0.00000591 | 1055 |
| Loss of Function | 3.31 | 8 | 26.4 | 0.304 | 0.00000129 | 339 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000618 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Poly(A) nuclease with 3'-5' RNase activity. Catalytic 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. Involved in mRNA decay mediated by the major-protein- coding determinant of instability (mCRD) of the FOS gene in the cytoplasm. In the presence of ZNF335, enhances ligand-dependent transcriptional activity of nuclear hormone receptors, including RARA. The increase of ligand-dependent ESR1-mediated transcription is much smaller, if any. Mediates cell proliferation and cell survival and prevents cellular senescence. {ECO:0000269|PubMed:11889047, ECO:0000269|PubMed:18180299, ECO:0000269|PubMed:20065043, ECO:0000269|PubMed:21233283}.;
- Pathway
- RNA degradation - Homo sapiens (human);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;TP53 Regulates Transcription of Cell Cycle Genes;Transcriptional Regulation by TP53;Deadenylation of mRNA;Deadenylation-dependent mRNA decay
(Consensus)
Recessive Scores
- pRec
- 0.127
Intolerance Scores
- loftool
- 0.315
- rvis_EVS
- -0.29
- rvis_percentile_EVS
- 33.2
Haploinsufficiency Scores
- pHI
- 0.461
- hipred
- Y
- hipred_score
- 0.745
- ghis
- 0.661
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.908
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cnot6
- Phenotype
- skeleton phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- 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;positive regulation of cell population proliferation;positive regulation of cytoplasmic mRNA processing body assembly;gene silencing by miRNA;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;nuclear-transcribed mRNA catabolic process, no-go decay;RNA phosphodiester bond hydrolysis, exonucleolytic;positive regulation of nuclear receptor transcription coactivator activity
- Cellular component
- nucleus;cytosol;membrane;CCR4-NOT complex
- Molecular function
- RNA binding;exoribonuclease activity;poly(A)-specific ribonuclease activity;protein binding;metal ion binding