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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	4849
Gene name	CCR4-NOT transcription complex subunit 3
Gene symbol	CNOT3
Synonyms (NCBI Gene)	IDDSADFLENG2NOT3NOT3H
Chromosome	19
Chromosome location	19q13.42

Show/Hide all (1)

SNP ID	Visualize variation	Clinical significance	Consequence
rs753475896	C>-,CC,CCC	Uncertain-significance, pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant

Show/Hide all (26)

miRTarBase ID	miRNA	Experiments	Reference
MIRT051783	hsa-let-7c-5p	CLASH	23622248
MIRT039544	hsa-miR-652-3p	CLASH	23622248
MIRT038618	hsa-miR-185-3p	CLASH	23622248
MIRT900388	hsa-miR-1343	CLIP-seq
MIRT900389	hsa-miR-2115	CLIP-seq
MIRT900390	hsa-miR-3150a-3p	CLIP-seq
MIRT900391	hsa-miR-3175	CLIP-seq
MIRT900392	hsa-miR-3192	CLIP-seq
MIRT900393	hsa-miR-4313	CLIP-seq
MIRT900394	hsa-miR-4667-5p	CLIP-seq
MIRT900395	hsa-miR-4700-5p	CLIP-seq
MIRT900396	hsa-miR-4728-5p	CLIP-seq
MIRT900397	hsa-miR-4779	CLIP-seq
MIRT900398	hsa-miR-486-3p	CLIP-seq
MIRT900399	hsa-miR-516a-3p	CLIP-seq
MIRT900400	hsa-miR-765	CLIP-seq
MIRT900401	hsa-miR-939	CLIP-seq
MIRT900388	hsa-miR-1343	CLIP-seq
MIRT900389	hsa-miR-2115	CLIP-seq
MIRT900392	hsa-miR-3192	CLIP-seq
MIRT2202759	hsa-miR-4525	CLIP-seq
MIRT2202760	hsa-miR-4716-3p	CLIP-seq
MIRT900397	hsa-miR-4779	CLIP-seq
MIRT900398	hsa-miR-486-3p	CLIP-seq
MIRT900399	hsa-miR-516a-3p	CLIP-seq
MIRT900400	hsa-miR-765	CLIP-seq

Show/Hide all (23)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000289	Process	Nuclear-transcribed mRNA poly(A) tail shortening	IBA
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:0001829	Process	Trophectodermal cell differentiation	IEA
GO:0005515	Function	Protein binding	IPI	10637334, 12207886, 16189514, 16778766, 17452450, 18377426, 20211142, 21981923, 21984185, 24736845, 26496610, 28514442, 31515488, 32296183, 32814053, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006417	Process	Regulation of translation	IEA
GO:0030014	Component	CCR4-NOT complex	IDA	19558367
GO:0030014	Component	CCR4-NOT complex	NAS	19558367
GO:0030015	Component	CCR4-NOT core complex	IBA
GO:0030015	Component	CCR4-NOT core complex	IEA
GO:0031047	Process	Regulatory ncRNA-mediated gene silencing	IEA
GO:0120162	Process	Positive regulation of cold-induced thermogenesis	IEA
GO:0120162	Process	Positive regulation of cold-induced thermogenesis	ISS	28032897
GO:2000036	Process	Regulation of stem cell population maintenance	IBA
GO:2000036	Process	Regulation of stem cell population maintenance	IEA
GO:2000036	Process	Regulation of stem cell population maintenance	IMP	22367759

MIM	HGNC	e!Ensembl
604910	7879	ENSG00000088038

O75175

Protein name

CCR4-NOT transcription complex subunit 3 (CCR4-associated factor 3) (Leukocyte receptor cluster member 2)

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

4C0D , 4C0G , 5FU6 , 5FU7 , 9C3H , 9C3I

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04065	Not3	3 → 232	Not1 N-terminal domain, CCR4-Not complex component	Family
PF04153	NOT2_3_5	620 → 747	NOT2 / NOT3 / NOT5 family	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitous. Highly expressed in brain, heart, thymus, spleen, kidney, liver, small intestine, lung and peripheral blood leukocytes. {ECO:0000269|PubMed:10637334}.

Sequence

MADKRKLQGEIDRCLKKVSEGVEQFEDIWQKLHNAANANQKEKYEADLKKEIKKLQRLRD
QIKTWVASNEIKDKRQLIDNRKLIETQMERFKVVERETKTKAYSKEGLGLAQKVDPAQKE
KEEVGQWLTNTIDTLNMQVDQFESEVESLSVQTRKKKGDKDKQDRIEGLKRHIEKHRYHV
RMLETILRMLDNDSILVDAIRKIKDDVEYYVDSSQDPDFEENEFLYDDLDLEDIPQALVA
TSPPSHSHMEDEIFNQSSSTPTSTTSSSPIPPSPANCTTENSEDDKKRGRSTDSEVSQSP
AKNGSKPVHSNQHPQSPAVPPTYPSGPPPAASALSTTPGNNGVPAPAAPPSALGPKASPA
PSHNSGTPAPYAQAVAPPAPSGPSTTQPRPPSVQPSGGGGGGSGGGGSSSSSNSSAGGGA
GKQNGATSYSSVVADSPAEVALSSSGGNNASSQALGPPSGPHNPPPSTSKEPSAAAPTGA
GGVAPGSGNNSGGPSLLVPLPVNPPSSPTPSFSDAKAAGALLNGPPQFSTAPEIKAPEPL
SSLKSMAERAAISSGIEDPVPTLHLTERDIILSSTSAPPASAQPPLQLSEVNIPLSLGVC
PLGPVPLTKEQLYQQAMEEAAWHHMPHPSDSERIRQYLPRNPCPTPPYHHQMPPPHSDTV
EFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFE
QGTYIYFDYEKWGQRKKEGFTFEYRYLEDRDLQ

Sequence length

753

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

Show/Hide Causal Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
CNOT3-associated disorder	Pathogenic	rs2075273330	RCV005622169
CNOT3-related disorder	Likely pathogenic; Pathogenic	rs2074547544, rs753475896	RCV003414162 RCV004751757
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies	Pathogenic; Likely pathogenic	rs2146638782, rs2146758722, rs2146646096, rs2518137990, rs2075273330, rs2517256882, rs2517294280, rs2514436908, rs2514116435, rs2514644148, rs2517525537, rs2518058484, rs2517611666, rs1213228037, rs2518542445 View all (7 more)	RCV001706941 RCV002249370 RCV002251052 RCV002286442 RCV002286457 RCV002290262 RCV002302842 RCV002472291 RCV002470305 RCV003232958 RCV003314128 RCV003315270 RCV004809995 RCV003988703 RCV003989449 RCV000856720 RCV000856721 RCV000856722 RCV000856723 RCV000856724 RCV002286829 RCV001254143
Moyamoya angiopathy with developmental delay	Likely pathogenic	rs2074638284, rs2074949880	RCV001261733 RCV001261734
See cases	Pathogenic	rs2514223066	RCV004584522

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Autism spectrum disorder	Likely benign	rs2517397124	RCV003127369
Colon adenocarcinoma	Benign	rs139874376	RCV005928454
Complex neurodevelopmental disorder	Conflicting classifications of pathogenicity	rs772101793, rs149108037	RCV005358101 RCV005367659
Intellectual disability	Conflicting classifications of pathogenicity; Uncertain significance; Likely benign	rs767913658, rs190206269, rs746808824	RCV001251949 RCV001251948 RCV001251950
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity	rs61743560	RCV005922761

Show/Hide Text Mining Associations (23)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alcohol Related Disorders	Associate	31201375
Arterial Occlusive Diseases	Stimulate	31474762
Autistic Disorder	Associate	34208845
Carcinoma Small Cell	Associate	31201375
Chronic Disease	Associate	34208845
Developmental Disabilities	Associate	31201375, 31474762
Dowling Degos Disease	Associate	31201375
Drug Hypersensitivity	Associate	30450575
Facies	Associate	34208845
Heart Defects Congenital	Associate	31474762
Hydrocephalus	Associate	40603987
Intellectual Disability	Associate	31201375, 31474762
Intracranial Arteriosclerosis	Associate	34073619
Keratoconus	Associate	36811882
Language Development Disorders	Associate	34208845
Mental Retardation Autosomal Recessive 7	Associate	34208845
Moyamoya disease 1	Associate	31474762
Multiple Myeloma	Associate	30809292
Muscle Hypotonia	Associate	31201375
Pathological Conditions Anatomical	Associate	34208845
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	27151989
Retinal Degeneration	Inhibit	23144630
Retinitis Pigmentosa	Associate	23144630, 24116917, 36338669

CNOT3 (CCR4-NOT transcription complex subunit 3)