CNOT10

gene
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Also known as FLJ12890FLJ13165

Summary

CNOT10 (CCR4-NOT transcription complex subunit 10, HGNC:23817) is a protein-coding gene on chromosome 3p22.3, encoding CCR4-NOT transcription complex subunit 10 (Q9H9A5). 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 regul….

Predicted to be involved in mRNA catabolic process and negative regulation of translation. Located in membrane. Part of CCR4-NOT complex.

Source: NCBI Gene 25904 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 111 total
  • Druggable target: yes
  • MANE Select transcript: NM_015442

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23817
Approved symbolCNOT10
NameCCR4-NOT transcription complex subunit 10
Location3p22.3
Locus typegene with protein product
StatusApproved
AliasesFLJ12890, FLJ13165
Ensembl geneENSG00000182973
Ensembl biotypeprotein_coding
OMIM620508
Entrez25904

Gene structure

Transcript identifiers

Ensembl transcripts: 48 — 34 protein_coding, 6 protein_coding_CDS_not_defined, 5 retained_intron, 3 nonsense_mediated_decay

ENST00000328834, ENST00000331889, ENST00000416457, ENST00000430408, ENST00000435630, ENST00000454516, ENST00000455381, ENST00000463697, ENST00000466103, ENST00000468599, ENST00000471003, ENST00000473064, ENST00000476967, ENST00000479397, ENST00000481526, ENST00000485136, ENST00000494439, ENST00000556853, ENST00000866038, ENST00000866039, ENST00000866040, ENST00000866041, ENST00000866042, ENST00000866043, ENST00000866044, ENST00000866045, ENST00000866046, ENST00000866047, ENST00000866048, ENST00000866049, ENST00000866050, ENST00000866051, ENST00000933338, ENST00000933339, ENST00000933340, ENST00000933341, ENST00000933342, ENST00000933343, ENST00000933344, ENST00000933345, ENST00000933346, ENST00000969495, ENST00000969496, ENST00000969497, ENST00000969498, ENST00000969499, ENST00000969500, ENST00000969501

RefSeq mRNA: 7 — MANE Select: NM_015442 NM_001256741, NM_001256742, NM_001393366, NM_001393367, NM_001393368, NM_001393369, NM_015442

CCDS: CCDS2655, CCDS58821, CCDS58822

Canonical transcript exons

ENST00000328834 — 19 exons

ExonStartEnd
ENSE000018758843277345732773875
ENSE000034911843273480032734976
ENSE000034969883270386832703962
ENSE000035014163270867032708820
ENSE000035229063273342332733544
ENSE000035263183276468232764809
ENSE000035334103271622532716311
ENSE000035464653272545032725599
ENSE000035653183272766832727870
ENSE000035743693272011432720231
ENSE000035775463276445532764490
ENSE000035892433275945832759571
ENSE000035983753271322732713369
ENSE000035984263271715432717237
ENSE000036215233276988732769962
ENSE000036407443270481132704972
ENSE000036532183276273332762863
ENSE000036533423273741032737490
ENSE000039309493268518832685482

Expression profiles

Bgee: expression breadth ubiquitous, 204 present calls, max score 94.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.5694 / max 270.4276, expressed in 1810 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
3589212.84111768
3589111.36631768
358890.8420592
358900.4070188
358950.092226
358930.01924
358940.00171

Top tissues by expression

250 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right testisUBERON:000453494.21gold quality
left testisUBERON:000453394.06gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047393.29gold quality
testisUBERON:000047392.65gold quality
right uterine tubeUBERON:000130291.59gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099191.51gold quality
ventricular zoneUBERON:000305391.43gold quality
adenohypophysisUBERON:000219691.28gold quality
colonic epitheliumUBERON:000039791.10gold quality
ganglionic eminenceUBERON:000402390.85gold quality
mucosa of transverse colonUBERON:000499190.67gold quality
skin of abdomenUBERON:000141689.94gold quality
skin of legUBERON:000151189.88gold quality
bone marrow cellCL:000209289.87gold quality
adrenal tissueUBERON:001830389.86gold quality
right ovaryUBERON:000211889.70gold quality
rectumUBERON:000105289.68gold quality
calcaneal tendonUBERON:000370189.64gold quality
cortical plateUBERON:000534389.64gold quality
granulocyteCL:000009489.53gold quality
right lobe of thyroid glandUBERON:000111989.34gold quality
body of pancreasUBERON:000115089.32gold quality
left ovaryUBERON:000211989.22gold quality
pituitary glandUBERON:000000789.14gold quality
leukocyteCL:000073889.11gold quality
monocyteCL:000057689.10gold quality
tibial nerveUBERON:000132389.00gold quality
spleenUBERON:000210688.96gold quality
metanephros cortexUBERON:001053388.90gold quality
body of uterusUBERON:000985388.81gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting CNOT10, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-477599.9875.006394
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-807599.9767.20962
HSA-MIR-590-3P99.9674.346478
HSA-MIR-365899.9673.874379
HSA-MIR-430799.8270.453374
HSA-MIR-3064-5P99.2666.131497
HSA-MIR-3085-3P99.2666.161490
HSA-MIR-6504-5P99.2665.951487
HSA-MIR-149-5P99.2567.161315
HSA-MIR-664A-3P99.2271.082696
HSA-MIR-607199.1667.771780
HSA-MIR-392698.9569.261438
HSA-MIR-4774-3P98.9067.82737
HSA-MIR-500A-5P98.7669.131241
HSA-MIR-548S98.5067.171213
HSA-MIR-63398.3569.451167
HSA-MIR-313297.9667.91711
HSA-MIR-197-5P97.2368.10596
HSA-MIR-479496.4765.531063
HSA-MIR-443595.9065.471201
HSA-MIR-664A-5P95.8464.93949

Literature-anchored findings (GeneRIF, showing 2)

  • CNOT11 interacts with the first amino acids of CNOT1 and with CNOT10 and is required for the association of CNOT10 with the CCR4-NOT complex. (PMID:23232451)
  • Human CNOT10 and CNOT11 form a complex that interacts with the CNOT1 N-terminal domain. (PMID:23303381)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriocnot10ENSDARG00000058528
mus_musculusCnot10ENSMUSG00000056167
rattus_norvegicusCnot10ENSRNOG00000052305
drosophila_melanogasterNot10FBGN0260444

Protein

Protein identifiers

CCR4-NOT transcription complex subunit 10Q9H9A5 (reviewed: Q9H9A5)

All UniProt accessions (5): Q9H9A5, E9PCN5, H7BZZ7, H7C0K1, H7C1X9

UniProt curated annotations — full annotation on UniProt →

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. Is not required for association of CNOT7 to the CCR4-NOT complex.

Subunit / interactions. Component of the CCR4-NOT complex; distinct complexes seem to exist that differ in the participation of probably mutually exclusive catalytic subunits. CNOT10 and CNOT11 form a subcomplex docked to the CNOT1 scaffold.

Subcellular location. Cytoplasm. Nucleus.

Similarity. Belongs to the CNOT10 family.

Isoforms (6)

UniProt IDNamesCanonical?
Q9H9A5-11yes
Q9H9A5-22
Q9H9A5-33
Q9H9A5-44
Q9H9A5-55
Q9H9A5-66

RefSeq proteins (7): NP_001243670, NP_001243671, NP_001380295, NP_001380296, NP_001380297, NP_001380298, NP_056257* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011990TPR-like_helical_dom_sfHomologous_superfamily
IPR019734TPR_rptRepeat
IPR039740CNOT10Family

UniProt features (70 total): helix 31, turn 8, sequence conflict 7, compositionally biased region 5, splice variant 5, region of interest 4, strand 4, sequence variant 2, initiator methionine 1, chain 1, modified residue 1, coiled-coil region 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
8FY3ELECTRON MICROSCOPY2.88
8BFIX-RAY DIFFRACTION3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H9A5-F179.870.60

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-429947Deadenylation of mRNA
R-HSA-6804115TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
R-HSA-9820841M-decay: degradation of maternal mRNAs by maternally stored factors

MSigDB gene sets: 91 (showing top): GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_TRANSLATION, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, REACTOME_DEADENYLATION_OF_MRNA, chr3p22, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_DEADENYLATION_DEPENDENT_DECAY, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GOBP_NUCLEAR_TRANSCRIBED_MRNA_POLY_A_TAIL_SHORTENING, REACTOME_METABOLISM_OF_RNA, GOBP_REGULATION_OF_TRANSLATION

GO Biological Process (5): nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289), mRNA catabolic process (GO:0006402), negative regulation of translation (GO:0017148), regulatory ncRNA-mediated gene silencing (GO:0031047), regulation of translation (GO:0006417)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), cytosol (GO:0005829), membrane (GO:0016020), CCR4-NOT complex (GO:0030014), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Deadenylation-dependent mRNA decay1
TP53 Regulates Transcription of Cell Cycle Genes1
Maternal to zygotic transition (MZT)1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
negative regulation of gene expression3
cellular anatomical structure3
translation2
nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay1
nuclear-transcribed mRNA catabolic process1
RNA catabolic process1
mRNA metabolic process1
regulation of translation1
negative regulation of protein metabolic process1
post-transcriptional regulation of gene expression1
regulation of protein metabolic process1
binding1
intracellular membrane-bounded organelle1
cytoplasm1
intracellular protein-containing complex1
intracellular anatomical structure1

Protein interactions and networks

STRING

1150 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CNOT10CNOT2Q9NZN8995
CNOT10CNOT1A5YKK6995
CNOT10CNOT3O75175995
CNOT10CNOT11Q9UKZ1994
CNOT10CNOT9Q92600994
CNOT10CNOT6Q9ULM6961
CNOT10CNOT7Q9UIV1959
CNOT10CNOT6LQ96LI5951
CNOT10CNOT8Q9UFF9915
CNOT10CNOT4O95628906
CNOT10VCF1Q969W3775
CNOT10CNOT12Q9C0C2714
CNOT10CCDC127Q96BQ5703
CNOT10TADA2BQ86TJ2649
CNOT10ZKSCAN5Q9Y2L8623

IntAct

122 interactions, top by confidence:

ABTypeScore
MED4MED19psi-mi:“MI:2364”(proximity)0.900
CNOT11CNOT1psi-mi:“MI:0914”(association)0.770
CNOT2CNOT1psi-mi:“MI:0914”(association)0.740
CNOT3CNOT1psi-mi:“MI:0914”(association)0.740
CNOT10CNOT11psi-mi:“MI:0915”(physical association)0.740
CNOT11CNOT10psi-mi:“MI:0915”(physical association)0.740
TOB1CNOT1psi-mi:“MI:0914”(association)0.710
TNRC6CCNOT1psi-mi:“MI:0914”(association)0.690
HTTCNOT10psi-mi:“MI:0915”(physical association)0.670
CNOT10CNOT6Lpsi-mi:“MI:0915”(physical association)0.660
CNOT6CNOT10psi-mi:“MI:0915”(physical association)0.660
CAPZBCNOT1psi-mi:“MI:0914”(association)0.640
CAPZA2CNOT1psi-mi:“MI:0914”(association)0.640
TNRC6CCNOT1psi-mi:“MI:0914”(association)0.620
CNOT10RAVER1psi-mi:“MI:0915”(physical association)0.560
TNRC6CCNOT10psi-mi:“MI:0915”(physical association)0.560

BioGRID (203): CNOT10 (Reconstituted Complex), CNOT10 (Affinity Capture-Western), CNOT10 (Affinity Capture-MS), CNOT10 (Affinity Capture-MS), CNOT10 (Affinity Capture-MS), CNOT10 (Affinity Capture-MS), CNOT10 (Affinity Capture-MS), CNOT10 (Affinity Capture-MS), CNOT10 (Proximity Label-MS), CNOT10 (Proximity Label-MS), CNOT10 (Proximity Label-MS), CNOT10 (Proximity Label-MS), CNOT10 (Proximity Label-MS), CNOT10 (Proximity Label-MS), CNOT10 (Proximity Label-MS)

ESM2 similar proteins: A0JN62, A2RT67, A2RUS2, A2VDU2, A4IFB6, A4IIM3, A7MBL8, B1H2P5, B4F779, O94967, P48553, Q08CL8, Q0VEJ0, Q14161, Q15650, Q3TLI0, Q4R350, Q5RAQ5, Q5RCP7, Q5RDV5, Q5TKA1, Q5XIA4, Q5ZIW2, Q5ZJK1, Q68CZ1, Q6AYF1, Q6QD73, Q7TSG1, Q7ZYH1, Q8BH15, Q8BIK4, Q8BKH7, Q8C735, Q8CG73, Q8CGF6, Q8IWR0, Q8IZQ1, Q8N6S4, Q8N960, Q8NEU8

Diamond homologs: A4IFB6, Q08CL8, Q4R350, Q5XIA4, Q5ZIW2, Q6DE97, Q6NU53, Q8BH15, Q9H9A5, Q9V3G6

SIGNOR signaling

1 interactions.

AEffectBMechanism
CNOT10“form complex”“CCR4-NOT complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 93 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain988.2×8e-14
Deadenylation of mRNA758.0×2e-09
M-decay: degradation of maternal mRNAs by maternally stored factors849.2×5e-10
Loss of Nlp from mitotic centrosomes618.0×6e-05
Loss of proteins required for interphase microtubule organization from the centrosome618.0×6e-05
AURKA Activation by TPX2617.2×7e-05
Recruitment of mitotic centrosome proteins and complexes615.4×1e-04
Regulation of PLK1 Activity at G2/M Transition614.4×1e-04

GO biological processes:

GO termPartnersFoldFDR
nuclear-transcribed mRNA poly(A) tail shortening770.2×2e-09
regulation of translation719.1×1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

111 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance78
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3081 predictions. Top by Δscore:

VariantEffectΔscore
3:32685480:CAGG:Cdonor_loss1.0000
3:32685481:AGG:Adonor_loss1.0000
3:32685482:GG:Gdonor_loss1.0000
3:32685483:GTAG:Gdonor_loss1.0000
3:32685484:T:Adonor_loss1.0000
3:32703963:G:GGdonor_gain1.0000
3:32704809:A:AGacceptor_gain1.0000
3:32704809:AGTCT:Aacceptor_gain1.0000
3:32704810:G:GGacceptor_gain1.0000
3:32704810:GTCT:Gacceptor_gain1.0000
3:32704810:GTCTG:Gacceptor_gain1.0000
3:32708667:TA:Tacceptor_loss1.0000
3:32708668:A:ACacceptor_loss1.0000
3:32708668:A:AGacceptor_gain1.0000
3:32708669:G:GGacceptor_gain1.0000
3:32708784:G:GGdonor_gain1.0000
3:32708818:TTGGT:Tdonor_loss1.0000
3:32708820:GGTA:Gdonor_loss1.0000
3:32708821:G:GGdonor_gain1.0000
3:32708821:GTA:Gdonor_loss1.0000
3:32708822:TAT:Tdonor_loss1.0000
3:32716223:AGACT:Aacceptor_gain1.0000
3:32716224:GA:Gacceptor_gain1.0000
3:32716224:GACT:Gacceptor_gain1.0000
3:32716224:GACTG:Gacceptor_gain1.0000
3:32717148:T:TAacceptor_gain1.0000
3:32717149:GACA:Gacceptor_loss1.0000
3:32717151:CA:Cacceptor_loss1.0000
3:32717152:A:AGacceptor_gain1.0000
3:32717153:G:Cacceptor_loss1.0000

AlphaMissense

4926 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:32717199:A:GK236E1.000
3:32717200:A:TK236I1.000
3:32717201:A:CK236N1.000
3:32717201:A:TK236N1.000
3:32717203:G:CR237T1.000
3:32717203:G:TR237M1.000
3:32717204:G:CR237S1.000
3:32717204:G:TR237S1.000
3:32717211:A:CK240Q1.000
3:32717211:A:GK240E1.000
3:32717212:A:TK240M1.000
3:32717213:G:CK240N1.000
3:32717213:G:TK240N1.000
3:32720135:A:GK256E1.000
3:32720137:A:CK256N1.000
3:32720137:A:TK256N1.000
3:32720138:A:CS257R1.000
3:32720140:C:AS257R1.000
3:32720140:C:GS257R1.000
3:32720147:G:AE260K1.000
3:32720172:A:TK268I1.000
3:32720173:A:CK268N1.000
3:32720173:A:TK268N1.000
3:32720174:G:CA269P1.000
3:32720175:C:AA269D1.000
3:32720180:A:GK271E1.000
3:32720184:T:CL272P1.000
3:32725481:C:AN298K1.000
3:32725481:C:GN298K1.000
3:32725483:T:CL299P1.000

dbSNP variants (sampled 300 via entrez): RS1000033811 (3:32771664 A>C), RS1000045875 (3:32730036 G>T), RS1000079858 (3:32692074 T>C), RS1000112149 (3:32764042 A>G), RS1000154190 (3:32724615 T>C), RS1000154839 (3:32684385 T>C), RS1000164036 (3:32684435 T>C), RS1000190693 (3:32773943 T>C), RS1000214484 (3:32684725 ATAAT>A), RS1000228484 (3:32695475 G>A,T), RS1000240792 (3:32731124 G>A), RS1000242584 (3:32689858 G>A), RS1000294550 (3:32730912 G>A), RS1000308834 (3:32700896 G>A), RS1000314781 (3:32771469 C>T)

Disease associations

OMIM: gene MIM:620508 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

StudyTraitp-value
GCST009310_25Sensorimotor dexterity9.000000e-06
GCST010396_189Gut microbiota (bacterial taxa, hurdle binary method)3.000000e-06
GCST012174_1Diabetic retinopathy in type 2 diabetes7.000000e-10

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0008354cognitive function measurement
EFO:0007874gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4105878 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects methylation, decreases expression2
Arsenicaffects methylation, decreases expression, increases abundance2
Cyclosporineincreases expression2
aristolochic acid Idecreases expression1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
sodium arsenitedecreases expression, increases abundance1
2,3,5-(triglutathion-S-yl)hydroquinoneincreases ADP-ribosylation1
abrineincreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Ivermectindecreases expression1
Plant Extractsaffects cotreatment, increases expression1
Cadmium Chloridedecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4012563BindingBinding affinity to CCR4-NOT transcription complex subunit 10 in human INA-6 cells after 3 hrs by nanoLC-MS/MS methodUgi Reaction-Derived α-Acyl Aminocarboxamides Bind to Phosphatidylinositol 3-Kinase-Related Kinases, Inhibit HSF1-Dependent Heat Shock Response, and Induce Apoptosis in Multiple Myeloma Cells. — J Med Chem

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): diabetic retinopathy