CNOT11

CCR4-NOT transcription complex subunit 11, the group of CCR4-NOT transcription complex

Basic information

Region (hg38): 2:101252886-101270316

Previous symbols: [ "C2orf29" ]

Links

ENSG00000158435 ∙ NCBI:55571 ∙ ∙ HGNC:25217 ∙ Uniprot:Q9UKZ1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CNOT11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNOT11 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				1		1
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in CNOT11

This is a list of pathogenic ClinVar variants found in the CNOT11 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-101252969-C-T		not specified	Uncertain significance (Dec 14, 2023)
2-101253122-G-C		not specified	Uncertain significance (Dec 21, 2023)
2-101253139-G-A		not specified	Uncertain significance (Jul 02, 2024)
2-101253144-G-T		not specified	Uncertain significance (Jun 25, 2024)
2-101253294-G-C		not specified	Uncertain significance (Jul 25, 2024)
2-101253313-C-G		not specified	Uncertain significance (Oct 04, 2022)
2-101253322-A-G		not specified	Uncertain significance (Sep 24, 2024)
2-101253436-C-G		not specified	Uncertain significance (Apr 23, 2024)
2-101257809-C-G		not specified	Uncertain significance (Jan 18, 2025)
2-101257880-C-T		not specified	Uncertain significance (Apr 13, 2023)
2-101257881-G-A		not specified	Uncertain significance (Dec 07, 2021)
2-101257885-G-C		not specified	Uncertain significance (Jan 10, 2022)
2-101257910-A-G		not specified	Uncertain significance (Jul 19, 2023)
2-101264875-C-T		not specified	Uncertain significance (Aug 22, 2023)
2-101264891-T-G		not specified	Uncertain significance (Jan 09, 2024)
2-101264923-C-T		not specified	Uncertain significance (Feb 23, 2025)
2-101264933-C-G		not specified	Uncertain significance (Mar 24, 2023)
2-101264953-A-C		not specified	Uncertain significance (Nov 15, 2024)
2-101266734-G-C		not specified	Uncertain significance (Jun 28, 2024)
2-101269106-T-C		not specified	Likely benign (Dec 04, 2024)
2-101269246-C-T		not specified	Uncertain significance (Dec 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNOT11	protein_coding	protein_coding	ENST00000289382	7	17515

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.597	0.403	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	174	283	0.615	0.0000152	3298
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000735	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000658	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• 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.
• Pathway: 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: 0.0908

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.510
• hipred: Y
• hipred_score: 0.662
• ghis: 0.627

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cnot11

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;cell population proliferation;gene silencing by RNA
• Cellular component: nucleus;cytosol;CCR4-NOT complex
• Molecular function: molecular_function;protein binding