CNOT7
CCR4-NOT transcription complex subunit 7, the group of CCR4-NOT transcription complex
Basic information
Region (hg38): 8:17224966-17246878
Previous symbols: [ "CAF1" ]
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 CNOT7 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 | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 2 | |||||
| Total | 0 | 0 | 8 | 1 | 1 |
Variants in CNOT7
This is a list of pathogenic ClinVar variants found in the CNOT7 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-17230748-T-C | not specified | Uncertain significance (Dec 12, 2023) | ||
| 8-17234811-G-A | not specified | Uncertain significance (Dec 02, 2022) | ||
| 8-17237307-A-C | not specified | Uncertain significance (Dec 04, 2024) | ||
| 8-17237314-T-C | not specified | Uncertain significance (Sep 25, 2024) | ||
| 8-17243133-T-C | not specified | Uncertain significance (Aug 02, 2023) | ||
| 8-17245065-C-T | not specified | Uncertain significance (May 15, 2024) | ||
| 8-17245134-C-A | not specified | Uncertain significance (Jun 14, 2022) | ||
| 8-17245139-G-A | not specified | Uncertain significance (Jul 09, 2021) | ||
| 8-17246633-C-G | Likely benign (Jul 27, 2018) | |||
| 8-17246679-G-A | Benign (Jun 16, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CNOT7 | protein_coding | protein_coding | ENST00000361272 | 6 | 17651 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00314 | 125723 | 0 | 2 | 125725 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.63 | 61 | 152 | 0.401 | 0.00000759 | 1884 |
| Missense in Polyphen | 9 | 50.301 | 0.17892 | 649 | ||
| Synonymous | -1.36 | 66 | 53.4 | 1.24 | 0.00000267 | 507 |
| Loss of Function | 3.82 | 0 | 17.0 | 0.00 | 9.65e-7 | 194 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Has 3'-5' poly(A) exoribonuclease activity for synthetic poly(A) RNA substrate. Its function seems to be partially redundant with that of CNOT8. 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. During miRNA-mediated repression the complex seems also to act as translational repressor during translational initiation. Additional complex functions may be a consequence of its influence on mRNA expression. Associates with members of the BTG family such as TOB1 and BTG2 and is required for their anti- proliferative activity. {ECO:0000269|PubMed:19605561, ECO:0000269|PubMed:20065043, ECO:0000269|PubMed:20634287, ECO:0000269|PubMed:23236473}.;
- 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
- 0.113
Intolerance Scores
- loftool
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.824
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.708
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.731
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cnot7
- Phenotype
- reproductive system phenotype; endocrine/exocrine gland phenotype; cellular phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;nuclear-transcribed mRNA poly(A) tail shortening;deadenylation-dependent decapping of nuclear-transcribed mRNA;carbohydrate metabolic process;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;signal transduction;positive regulation of cell population proliferation;negative regulation of cell population proliferation;negative regulation of gene expression;negative regulation of translation;gene silencing by RNA;cytoplasmic mRNA processing body assembly;gene silencing by miRNA;regulation of tyrosine phosphorylation of STAT protein;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;positive regulation of viral genome replication;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;defense response to virus;positive regulation of nuclear-transcribed mRNA poly(A) tail shortening;negative regulation of type I interferon-mediated signaling pathway;positive regulation of mRNA catabolic process;RNA phosphodiester bond hydrolysis, exonucleolytic;positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
- Cellular component
- P-body;nucleus;cytoplasm;cytosol;membrane;nuclear body;nuclear speck;CCR4-NOT complex;CCR4-NOT core complex;host cell PML body
- Molecular function
- 3'-5'-exoribonuclease activity;DNA-binding transcription factor activity;transcription corepressor activity;RNA binding;exoribonuclease activity;poly(A)-specific ribonuclease activity;protein binding;transcription factor binding;metal ion binding