Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	9125
Gene name	CCR4-NOT transcription complex subunit 9
Gene symbol	CNOT9
Synonyms (NCBI Gene)	CAF40CT129RCD-1RCD1RQCD1
Chromosome	2
Chromosome location	2q35
Summary	This gene encodes a member of the highly conserved RCD1 protein family. The encoded protein is a transcriptional cofactor and a core protein of the CCR4-NOT complex. It may be involved in signal transduction as well as retinoic acid-regulated cell differe

Show/Hide all (4)

SNP ID	Visualize variation	Clinical significance	Consequence
rs267599211	C>T	Likely-pathogenic	Coding sequence variant, intron variant, missense variant
rs1057519955	C>T	Likely-pathogenic	Missense variant, coding sequence variant, intron variant
rs1057519956	T>C	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1057519957	C>G	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant

Show/Hide all (30)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000289	Process	Nuclear-transcribed mRNA poly(A) tail shortening	NAS	31320642
GO:0000932	Component	P-body	IBA
GO:0000932	Component	P-body	IEA
GO:0000932	Component	P-body	ISS
GO:0003713	Function	Transcription coactivator activity	IDA	18180299
GO:0005154	Function	Epidermal growth factor receptor binding	IPI	20878056
GO:0005515	Function	Protein binding	IPI	18180299, 18377426, 20878056, 24768540, 28514442, 32296183, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006402	Process	MRNA catabolic process	IEA
GO:0006417	Process	Regulation of translation	IEA
GO:0007548	Process	Sex differentiation	TAS
GO:0016020	Component	Membrane	HDA	19946888
GO:0017148	Process	Negative regulation of translation	IBA
GO:0019221	Process	Cytokine-mediated signaling pathway	IEA
GO:0019900	Function	Kinase binding	IPI	20878056
GO:0019904	Function	Protein domain specific binding	IPI	24768540
GO:0030014	Component	CCR4-NOT complex	IDA	19558367
GO:0030014	Component	CCR4-NOT complex	IEA
GO:0030014	Component	CCR4-NOT complex	NAS	19558367
GO:0030015	Component	CCR4-NOT core complex	IBA
GO:0031047	Process	Regulatory ncRNA-mediated gene silencing	IEA
GO:0032991	Component	Protein-containing complex	IDA	20878056
GO:0033138	Process	Positive regulation of peptidyl-serine phosphorylation	IMP	20878056
GO:0033147	Process	Negative regulation of intracellular estrogen receptor signaling pathway	IMP	16778766
GO:0042803	Function	Protein homodimerization activity	IDA	24768540
GO:0045742	Process	Positive regulation of epidermal growth factor receptor signaling pathway	IMP	20878056
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA

MIM	HGNC	e!Ensembl
612054	10445	ENSG00000144580

Q92600

Protein name

CCR4-NOT transcription complex subunit 9 (Cell differentiation protein RQCD1 homolog) (Rcd-1)

Protein 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 initiati

PDB

2FV2 , 4CRU , 4CRV , 4CT6 , 4CT7 , 5LSW , 5ONA , 5ONB , 6HOM , 6HON , 9FL8

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04078	Rcd1	25 → 283		Family

Tissue specificity

TISSUE SPECIFICITY: Detected in spleen, thymus, prostate, testis, ovary and intestine. {ECO:0000269|PubMed:9447985}.

Sequence

MHSLATAAPVPTTLAQVDREKIYQWINELSSPETRENALLELSKKRESVPDLAPMLWHSF
GTIAALLQEIVNIYPSINPPTLTAHQSNRVCNALALLQCVASHPETRSAFLAAHIPLFLY
PFLHTVSKTRPFEYLRLTSLGVIGALVKTDEQEVINFLLTTEIIPLCLRIMESGSELSKT
VATFILQKILLDDTGLAYICQTYERFSHVAMILGKMVLQLSKEPSARLLKHVVRCYLRLS
DNPRAREALRQCLPDQLKDTTFAQVLKDDTTTKRWLAQLVKNLQEGQVTDPRGIPLPPQ

Sequence length

299

Interactions

View interactions

	KEGG		Reactome
	RNA degradation		Deadenylation of mRNA TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
CNOT9-associated neurodevelopmental disorder	Pathogenic; Likely pathogenic	rs981210817, rs2469453674, rs2469475477, rs267599211	RCV002286439 RCV002286459 RCV002286460 RCV002286407	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
COMPLEX NEURODEVELOPMENTAL DISORDER	—	CTD, ClinGen	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (20)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adenocarcinoma of prostate	Prostate adenocarcinoma	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	19724902		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cutaneous Melanoma	Melanoma	BEFREE	25544760		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cutaneous Melanoma	Melanoma	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	37092538	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	31797865	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	37092538	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Facial Dysmorphism with Multiple Malformations	Facial dysmorphism syndrome	Pubtator	37092538	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Gastric Adenocarcinoma	Gastric Cancer	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	37092538	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	19724902		★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	25544760		★★★★★ ★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	25544760	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Melanoma Cutaneous Malignant	Melanoma	Pubtator	25544760	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	25544760, 29924958		★★★★★ ★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	37092538	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Transitional cell carcinoma of bladder	Bladder carcinoma	CLINVAR_DG	26619011		★★★★★ ★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple Negative Breast Neoplasms	BEFREE	29924958		★★★★★ ★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	29924958	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

CNOT9 (CCR4-NOT transcription complex subunit 9)