CNOT4

CCR4-NOT transcription complex subunit 4, the group of CCR4-NOT transcription complex|Ring finger proteins|RNA binding motif containing

Basic information

Region (hg38): 7:135361795-135510145

Previous symbols: [ "NOT4" ]

Links

ENSG00000080802

∙ NCBI:4850 ∙ OMIM:604911 ∙ HGNC:7880 ∙ Uniprot:O95628 ∙ 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 CNOT4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNOT4 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			14 clinvar			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in CNOT4

This is a list of pathogenic ClinVar variants found in the CNOT4 region.

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

Position	Phenotype	Significance	ClinVar
7-135362923-T-G	not specified	Uncertain significance (Sep 11, 2024)	3494492
7-135362941-G-T	not specified	Uncertain significance (Apr 19, 2024)	3268222
7-135362964-G-T	not specified	Uncertain significance (Jul 09, 2021)	2235531
7-135362988-G-A	not specified	Uncertain significance (Jan 27, 2022)	2274194
7-135363022-C-T	not specified	Uncertain significance (Apr 05, 2023)	2533279
7-135363082-C-G	not specified	Uncertain significance (Sep 20, 2023)	3146625
7-135363153-G-C	not specified	Uncertain significance (Jun 12, 2023)	2518682
7-135363905-T-C	not specified	Uncertain significance (Feb 10, 2022)	2276561
7-135363934-G-A	not specified	Uncertain significance (Mar 30, 2024)	3268221
7-135363965-A-C	not specified	Uncertain significance (Mar 30, 2024)	3268220
7-135363985-T-C	not specified	Uncertain significance (Mar 30, 2024)	3268219
7-135363991-T-G	not specified	Uncertain significance (Aug 07, 2024)	3494491
7-135364034-T-C	not specified	Uncertain significance (Oct 12, 2024)	3494494
7-135394025-C-G	not specified	Uncertain significance (Dec 01, 2022)	2371174
7-135394076-C-T	not specified	Uncertain significance (Feb 28, 2024)	3146623
7-135394131-A-T	not specified	Uncertain significance (Mar 30, 2024)	3268218
7-135394137-A-G	not specified	Uncertain significance (Mar 30, 2024)	3268217
7-135394170-C-T	not specified	Uncertain significance (May 20, 2024)	3268216
7-135394212-T-C	not specified	Uncertain significance (Oct 19, 2024)	3146622
7-135394221-G-A	not specified	Uncertain significance (Jul 02, 2024)	3494490
7-135394239-G-C	not specified	Uncertain significance (Feb 02, 2024)	3146621
7-135394242-A-G	not specified	Uncertain significance (Apr 20, 2024)	3268225
7-135394260-G-C	not specified	Uncertain significance (Jul 13, 2021)	2236646
7-135395772-T-C	not specified	Uncertain significance (Apr 26, 2024)	3268226
7-135395795-C-T	not specified	Uncertain significance (Jan 23, 2024)	3146627

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNOT4	protein_coding	protein_coding	ENST00000541284	11	148329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000395	114657	0	1	114658	0.00000436

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.49	207	405	0.512	0.0000217	4688
Missense in Polyphen		45	153.58	0.293		1801
Synonymous	0.348	147	152	0.964	0.00000867	1394
Loss of Function	5.17	1	33.1	0.0302	0.00000181	364

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)	0.00000945	0.00000945
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Has E3 ubiquitin ligase activity, promoting ubiquitination and degradation of target proteins (PubMed:11823428, PubMed:22159038, PubMed:26575292). Involved in activation of the JAK/STAT pathway (PubMed:11823428, PubMed:22159038). Catalyzes ubiquitination of methylated RBM15 (PubMed:26575292). {ECO:0000269|PubMed:11823428, ECO:0000269|PubMed:22159038, ECO:0000269|PubMed:26575292}.;
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: 0.133

Intolerance Scores

loftool: 0.120
rvis_EVS: 0.04
rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

pHI: 0.638
hipred: Y
hipred_score: 0.843
ghis: 0.576

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.912

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cnot4
Phenotype: hematopoietic system 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); immune system phenotype; skeleton phenotype; limbs/digits/tail phenotype;

Gene ontology

Biological process: nuclear-transcribed mRNA poly(A) tail shortening;ubiquitin-dependent protein catabolic process;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;protein ubiquitination;regulation of megakaryocyte differentiation;protein autoubiquitination
Cellular component: nucleus;cytosol;CCR4-NOT complex
Molecular function: RNA binding;ubiquitin-protein transferase activity;protein binding;metal ion binding