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

ENSG00000198791NCBI:29883OMIM:604913HGNC:14101Uniprot:Q9UIV1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CNOT7 gene.

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
clinvar
8
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
clinvar
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)3146638
8-17234811-G-A not specified Uncertain significance (Dec 02, 2022)2332331
8-17237307-A-C not specified Uncertain significance (Dec 04, 2024)3494508
8-17237314-T-C not specified Uncertain significance (Sep 25, 2024)3494506
8-17243133-T-C not specified Uncertain significance (Aug 02, 2023)2615724
8-17245065-C-T not specified Uncertain significance (May 15, 2024)3268232
8-17245134-C-A not specified Uncertain significance (Jun 14, 2022)2291464
8-17245139-G-A not specified Uncertain significance (Jul 09, 2021)2412376
8-17246633-C-G Likely benign (Jul 27, 2018)1219001
8-17246679-G-A Benign (Jun 16, 2018)671125

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CNOT7protein_codingprotein_codingENST00000361272 617651
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9970.00314125723021257250.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.63611520.4010.000007591884
Missense in Polyphen950.3010.17892649
Synonymous-1.366653.41.240.00000267507
Loss of Function3.82017.00.009.65e-7194

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001760.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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