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GeneE
26 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
CNOT1
CCR4-NOT transcription complex subunit 1
Chromosome 16 Β· 16q21
NCBI Gene: 23019Ensembl: ENSG00000125107.20HGNC: HGNC:7877UniProt: A5YKK6
220PubMed Papers
22Diseases
0Drugs
45Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
RESEARCH IMPACT
Trending
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
poly(A)-specific ribonuclease activityRNA bindingprotein bindingprotein domain specific bindingholoprosencephaly 12 with or without pancreatic agenesisVissers-Bodmer syndromegenetic disordercomplex neurodevelopmental disorder
✦AI Summary

CNOT1 is the central scaffolding component of the CCR4-NOT complex, a master regulator of gene expression and mRNA stability 1. The complex functions as a major cellular mRNA deadenylase, with CNOT1 serving as a structural platform that recruits catalytic subunits and RNA-binding proteins to target mRNAs 2. CNOT1 mediates CCR4-NOT recruitment through multiple mechanisms: direct interaction with YTHDF2 readers of m6A-modified RNA 3, tRNA-dependent recruitment during translation 4, and P-body docking interactions 5. As a transcriptional corepressor, CNOT1 interacts with nuclear receptors to suppress gene expression, exemplified by its role in progesterone receptor signaling where it represses contractile genes in the myometrium 6. Clinically, de novo CNOT1 variants cause neurodevelopmental delay with intellectual disability, motor delay, speech delay, seizures, and behavioral problems, with evidence suggesting haploinsufficient mechanisms rather than dominant-negative effects 1. CNOT1 mutations also cause neonatal diabetes mellitus, identified among six novel NDM genes discovered between 2018-2024 7. Functional studies demonstrate that CNOT1 depletion broadly increases mRNA abundance and decreases decay rates genome-wide, with effects correlating to codon optimality 8, establishing CNOT1 as essential for normal human development and glucose homeostasis.

Sources cited
1
De novo CNOT1 variants cause neurodevelopmental delay with intellectual disability, motor delay, seizures, and behavioral problems; evidence supports haploinsufficient mechanisms
PMID: 32553196
2
CNOT1 forms the structural platform of the N-terminal CCR4-NOT module and facilitates protein-protein interactions
PMID: 36586408
3
CNOT1 recruits CCR4-NOT complex through direct interaction with YTHDF2 m6A readers for mRNA deadenylation
PMID: 27558897
4
Specific arginine tRNAs interact with CNOT3 and promote CCR4-NOT recruitment to translating ribosomes for mRNA decay
PMID: 39571015
5
CNOT1 mediates P-body docking with stress granules
PMID: 38536035
6
CNOT1 functions as a corepressor for progesterone receptor signaling to suppress contractile gene expression in myometrium
PMID: 38897566
7
CNOT1 mutations identified as a novel cause of neonatal diabetes mellitus between 2018-2024
PMID: 39344692
8
CNOT1 depletion broadly increases mRNA abundance and decreases global mRNA decay; effects correlate with codon optimality
PMID: 41161383
Disease Associationsβ“˜22
holoprosencephaly 12 with or without pancreatic agenesisOpen Targets
0.75Strong
Vissers-Bodmer syndromeOpen Targets
0.68Moderate
genetic disorderOpen Targets
0.51Moderate
complex neurodevelopmental disorderOpen Targets
0.47Moderate
neurodegenerative diseaseOpen Targets
0.47Moderate
Neurodevelopmental delayOpen Targets
0.46Moderate
Neurodevelopmental disorderOpen Targets
0.40Moderate
Global developmental delayOpen Targets
0.37Weak
schizophreniaOpen Targets
0.35Weak
Intellectual disabilityOpen Targets
0.27Weak
Alopecia-intellectual disability syndromeOpen Targets
0.27Weak
chronic laryngitisOpen Targets
0.25Weak
autism spectrum disorderOpen Targets
0.24Weak
Parkinson diseaseOpen Targets
0.24Weak
obesityOpen Targets
0.22Weak
glomerulonephritisOpen Targets
0.17Weak
Preterm intraventricular hemorrhageOpen Targets
0.12Weak
osteosarcomaOpen Targets
0.08Suggestive
infectionOpen Targets
0.06Suggestive
atherosclerosisOpen Targets
0.06Suggestive
Holoprosencephaly 12 with or without pancreatic agenesisUniProt
Vissers-Bodmer syndromeUniProt
Pathogenic Variants45
NM_016284.5(CNOT1):c.76C>T (p.Arg26Ter)Pathogenic
Vissers-Bodmer syndrome|See cases|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 26
NM_016284.5(CNOT1):c.1603C>T (p.Arg535Cys)Pathogenic
Holoprosencephaly sequence|Holoprosencephaly 12 with or without pancreatic agenesis|Vissers-Bodmer syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 535
NM_016284.5(CNOT1):c.4800+1G>APathogenic
Complex neurodevelopmental disorder|Vissers-Bodmer syndrome
β˜…β˜†β˜†β˜†2026
NM_016284.5(CNOT1):c.144dup (p.Arg49fs)Pathogenic
Vissers-Bodmer syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 49
NM_016284.5(CNOT1):c.1216-2A>GLikely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025
NM_016284.5(CNOT1):c.120_127del (p.Pro41fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 41
NM_016284.5(CNOT1):c.394dup (p.Ala132fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 132
NM_016284.5(CNOT1):c.5749dup (p.Gln1917fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 1917
NM_016284.5(CNOT1):c.6959G>A (p.Trp2320Ter)Pathogenic
Vissers-Bodmer syndrome
β˜…β˜†β˜†β˜†2025β†’ Residue 2320
NM_016284.5(CNOT1):c.3202-2dupLikely pathogenic
Holoprosencephaly 12 with or without pancreatic agenesis;Vissers-Bodmer syndrome
β˜…β˜†β˜†β˜†2025
NM_016284.5(CNOT1):c.920del (p.Gly307fs)Likely pathogenic
Vissers-Bodmer syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 307
NM_016284.5(CNOT1):c.2853T>G (p.Tyr951Ter)Likely pathogenic
Vissers-Bodmer syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 951
NM_016284.5(CNOT1):c.2560C>T (p.Arg854Ter)Likely pathogenic
Vissers-Bodmer syndrome
β˜…β˜†β˜†β˜†2024β†’ Residue 854
NM_016284.5(CNOT1):c.2834del (p.Pro945fs)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2024β†’ Residue 945
NM_016284.5(CNOT1):c.1272T>G (p.Tyr424Ter)Likely pathogenic
CNOT1-related disorder
β˜…β˜†β˜†β˜†2024β†’ Residue 424
NM_016284.5(CNOT1):c.434-2A>TLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_016284.5(CNOT1):c.4434+1delLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2023
NM_016284.5(CNOT1):c.2751dup (p.Gly918fs)Likely pathogenic
CNOT1-related disorder
β˜…β˜†β˜†β˜†2023β†’ Residue 918
NM_016284.5(CNOT1):c.439C>T (p.Gln147Ter)Likely pathogenic
Vissers-Bodmer syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 147
NM_016284.5(CNOT1):c.445dup (p.Ile149fs)Pathogenic
Vissers-Bodmer syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 149
View on ClinVar β†—
Related Genes
MMP7Protein interaction100%CNOT4Protein interaction100%CPEB3Protein interaction100%TNRC6AProtein interaction100%CNOT10Protein interaction100%CNOT11Protein interaction100%
Tissue Expression6 tissues
Brain
100%
Lung
76%
Heart
72%
Ovary
61%
Bone Marrow
60%
Liver
47%
Gene Interaction Network
Click a node to explore
CNOT1MMP7CNOT4CPEB3TNRC6ACNOT10CNOT11
PROTEIN STRUCTURE
Preparing viewer…
PDB4J8S Β· 1.55 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.06Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.04 [0.02–0.06]
RankingsWhere CNOT1 stands among ~20K protein-coding genes
  • #1,865of 20,598
    Most Researched220 Β· top 10%
  • #1,417of 5,498
    Most Pathogenic Variants45
  • #12of 17,882
    Most Constrained (LOEUF)0.06 Β· top 1%
Genes detectedCNOT1
Sources retrieved26 papers
Response timeβ€”
πŸ“„ Sources
26β–Ό
1
De Novo Variants in CNOT1, a Central Component of the CCR4-NOT Complex Involved in Gene Expression and RNA and Protein Stability, Cause Neurodevelopmental Delay.
PMID: 32553196
Am J Hum Genet Β· 2020
1.00
2
Neonatal diabetes mellitus around the world: Update 2024.
PMID: 39344692
J Diabetes Investig Β· 2024
0.90
3
DDX6 modulates P-body and stress granule assembly, composition, and docking.
PMID: 38536035
J Cell Biol Β· 2024
0.80
4
Species-specific FMRP regulation of RACK1 is critical for prenatal cortical development.
PMID: 37820724
Neuron Β· 2023
0.76
5
PMID: 41911374
0.72