CNOT6L

CCR4-NOT transcription complex subunit 6 like, the group of CCR4-NOT transcription complex

Basic information

Region (hg38): 4:77713387-77819615

Links

ENSG00000138767 ∙ NCBI:246175 ∙ OMIM:618069 ∙ HGNC:18042 ∙ Uniprot:Q96LI5 ∙ 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 CNOT6L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNOT6L 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			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	1	0

Variants in CNOT6L

This is a list of pathogenic ClinVar variants found in the CNOT6L region.

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

Position	Type	Phenotype	Significance	ClinVar
4-77720439-G-A		not specified	Uncertain significance (Nov 09, 2023)
4-77720442-T-C		not specified	Uncertain significance (Mar 02, 2023)
4-77720480-G-T		not specified	Uncertain significance (May 04, 2023)
4-77720552-T-C		not specified	Uncertain significance (Nov 14, 2024)
4-77720559-C-G		not specified	Uncertain significance (Jan 22, 2024)
4-77720573-G-C		not specified	Uncertain significance (Feb 15, 2023)
4-77726202-A-G			Likely benign (Jun 29, 2018)
4-77726273-T-C		not specified	Uncertain significance (Oct 04, 2022)
4-77726288-A-G		not specified	Uncertain significance (Aug 16, 2022)
4-77728897-G-C		not specified	Uncertain significance (Aug 04, 2024)
4-77728905-T-G		not specified	Uncertain significance (Apr 04, 2023)
4-77729055-T-G		not specified	Uncertain significance (Jul 27, 2024)
4-77742160-T-C		not specified	Uncertain significance (Nov 14, 2024)
4-77742234-T-G		not specified	Uncertain significance (Nov 10, 2022)
4-77742243-C-A		not specified	Uncertain significance (Aug 19, 2024)
4-77748321-G-A		not specified	Uncertain significance (May 27, 2022)
4-77748336-C-T		not specified	Uncertain significance (Dec 27, 2023)
4-77756924-T-C		not specified	Uncertain significance (Aug 02, 2021)
4-77774635-C-T		not specified	Uncertain significance (Mar 28, 2024)
4-77774665-G-A		not specified	Uncertain significance (Jul 20, 2021)
4-77774684-A-C		not specified	Uncertain significance (Nov 21, 2022)
4-77774704-C-T		not specified	Uncertain significance (Apr 25, 2022)
4-77776309-T-G		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNOT6L	protein_coding	protein_coding	ENST00000264903	12	106229

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00179	124634	0	5	124639	0.0000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.61	119	293	0.406	0.0000150	3635
Missense in Polyphen		21	125.05	0.16793		1570
Synonymous	0.721	100	110	0.912	0.00000579	1040
Loss of Function	4.49	2	27.3	0.0733	0.00000133	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.0000556	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has 3'-5' poly(A) exoribonuclease activity for synthetic poly(A) RNA substrate. 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. May be involved in the deadenylation-dependent degradation of mRNAs through the 3'-UTR AU-rich element-mediated mechanism. Involved in deadenylation-dependent degradation of CDKN1B mRNA. Its mRNA deadenylase activity can be inhibited by TOB1. Mediates cell proliferation and cell survival and prevents cellular senescence. {ECO:0000269|PubMed:17452450, 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)

Intolerance Scores

• loftool: 0.505
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.484
• hipred: Y
• hipred_score: 0.662
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cnot6l

Gene ontology

• Biological process: nuclear-transcribed mRNA poly(A) tail shortening;mRNA processing;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 RNA;mRNA destabilization;RNA phosphodiester bond hydrolysis, exonucleolytic
• Cellular component: nucleus;cytoplasm;cytosol;CCR4-NOT complex
• Molecular function: poly(A)-specific ribonuclease activity;protein binding;metal ion binding