CNOT9

CCR4-NOT transcription complex subunit 9, the group of CCR4-NOT transcription complex|Armadillo like helical domain containing

Basic information

Region (hg38): 2:218568580-218597080

Previous symbols: [ "RQCD1" ]

Links

ENSG00000144580

∙ NCBI:9125 ∙ OMIM:612054 ∙ HGNC:10445 ∙ Uniprot:Q92600 ∙ 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 CNOT9 gene.

not provided (1 variants)
Neurodevelopmental delay (1 variants)
CNOT9-associated neurodevelopmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNOT9 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	1 clinvar	3 clinvar	1 clinvar			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	3	1	0	0

Variants in CNOT9

This is a list of pathogenic ClinVar variants found in the CNOT9 region.

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

Position	Phenotype	Significance	ClinVar
2-218580672-C-G	CNOT9-associated neurodevelopmental disorder	Likely pathogenic (Sep 28, 2022)	1707499
2-218580673-G-A		Uncertain significance (Nov 28, 2022)	2503367
2-218583025-T-C	Transitional cell carcinoma of the bladder • Gastric adenocarcinoma • Malignant melanoma of skin • Hepatocellular carcinoma • Prostate adenocarcinoma	Likely pathogenic (May 31, 2016)	376526
2-218583026-C-G	Transitional cell carcinoma of the bladder • Prostate adenocarcinoma • Gastric adenocarcinoma • Malignant melanoma of skin • Hepatocellular carcinoma	Likely pathogenic (May 31, 2016)	376527
2-218584682-C-T	Malignant melanoma of skin	Likely pathogenic (May 31, 2016)	376525
2-218584683-C-T	Malignant melanoma of skin • CNOT9-associated neurodevelopmental disorder	Likely pathogenic (Sep 28, 2022)	74445
2-218592371-A-G		Uncertain significance (Feb 12, 2024)	3369013
2-218592656-G-A	CNOT9-associated neurodevelopmental disorder	Likely pathogenic (May 04, 2023)	1707500
2-218592656-G-C		Uncertain significance (Jun 01, 2023)	3343500
2-218594250-C-T	CNOT9-associated neurodevelopmental disorder • Neurodevelopmental delay	Pathogenic (Sep 28, 2022)	1706475

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNOT9	protein_coding	protein_coding	ENST00000273064	8	28501

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.986	0.0143	125739	0	2	125741	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.28	48	167	0.287	0.00000916	1919
Missense in Polyphen		6	64.515	0.093001		832
Synonymous	1.32	50	63.3	0.789	0.00000322	615
Loss of Function	3.63	1	17.3	0.0579	9.60e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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. Involved in down-regulation of MYB- and JUN-dependent transcription. May play a role in cell differentiation (By similarity). Can bind oligonucleotides, such as poly-G, poly-C or poly-T (in vitro), but the physiological relevance of this is not certain. Does not bind poly-A. Enhances ligand-dependent transcriptional activity of nuclear hormone receptors, including RARA, expect ESR1-mediated transcription that is not only slightly increased, if at all. {ECO:0000250, ECO:0000269|PubMed:17189474, ECO:0000269|PubMed:18180299}.;
Pathway: RNA degradation - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;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: 0.152

Intolerance Scores

loftool
rvis_EVS: -0.12
rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

pHI: 0.404
hipred: Y
hipred_score: 0.783
ghis: 0.723

Mouse Genome Informatics

Gene name: Cnot9
Phenotype: homeostasis/metabolism phenotype; embryo phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process: nuclear-transcribed mRNA poly(A) tail shortening;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;sex differentiation;negative regulation of translation;cytokine-mediated signaling pathway;gene silencing by RNA;positive regulation of peptidyl-serine phosphorylation;negative regulation of intracellular estrogen receptor signaling pathway;positive regulation of epidermal growth factor receptor signaling pathway;positive regulation of nuclear receptor transcription coactivator activity
Cellular component: P-body;nucleus;cytosol;membrane;CCR4-NOT complex;CCR4-NOT core complex;protein-containing complex
Molecular function: epidermal growth factor receptor binding;protein binding;kinase binding;protein domain specific binding;protein homodimerization activity