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10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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CNOT3
CCR4-NOT transcription complex subunit 3
Chromosome 19 Β· 19q13.42
NCBI Gene: 4849Ensembl: ENSG00000088038.20HGNC: HGNC:7879UniProt: B7Z6J7
115PubMed Papers
1Diseases
0Drugs
70Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTranscription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingregulation of stem cell population maintenanceCCR4-NOT complexpositive regulation of cold-induced thermogenesisIntellectual developmental disorder with speech delay, autism and dysmorphic facies
✦AI Summary

CNOT3 is a core subunit of the CCR4-NOT deadenylase complex, a major regulator of mRNA stability and gene expression. As a component of this complex, CNOT3 mediates bulk mRNA degradation, miRNA-mediated repression, and translational control 1. Mechanistically, CNOT3 recognizes stalled ribosomes during translation elongation through interaction with specific arginine tRNAs, which promote its recruitment to translating ribosomes and accelerate mRNA degradation in a codon usage-dependent manner 12. CNOT3 also inserts into the ribosomal E site and locks the L1 stalk to enforce translational stalling 2. Beyond mRNA decay, CNOT3 is essential for maintaining embryonic stem cell identity by repressing trophectoderm differentiation factors 3. Clinically, CNOT3 dysfunction is implicated in two distinct disease contexts. Heterozygous loss-of-function mutations in CNOT3 cause intellectual developmental disorder with speech delay, autism, and dysmorphic facies (IDDSADF), affecting 87% of patients with mild-to-moderate intellectual disability and behavioral issues 45. Additionally, elevated CNOT3 expression correlates with unfavorable outcomes in acute myeloid leukemia patients; CNOT3 promotes leukemogenesis by enhancing translation efficiency of c-MYC and other oncogenic targets through selective codon usage-dependent mechanisms 6. These findings establish CNOT3 as a critical regulator of post-transcriptional gene expression with significant roles in neural development and cancer pathogenesis.

Sources cited
1
Specific arginine tRNAs recruit CNOT3 to ribosomes during translation, promoting mRNA decay in a codon-dependent manner
PMID: 39571015
2
CNOT3 recognizes stalled ribosomes, inserts into the E site, and locks the L1 stalk to inhibit translation and couple it with mRNA decay
PMID: 37653243
3
CNOT3 maintains embryonic stem cell identity and prevents differentiation into extraembryonic lineages
PMID: 22367759
4
Heterozygous CNOT3 variants cause neurodevelopmental disorder with developmental delays, intellectual disability in 87% of patients, autism, and dysmorphic features
PMID: 40562808
5
Loss-of-function CNOT3 mutations cause intellectual developmental disorder with speech delay, autism, and dysmorphic facies; provides clinical characterization and novel variants
PMID: 36802310
6
Elevated CNOT3 expression promotes acute myeloid leukemia through translational regulation of c-MYC in a codon usage-dependent manner
PMID: 38491013
Disease Associationsβ“˜1
Intellectual developmental disorder with speech delay, autism and dysmorphic faciesUniProt
Pathogenic Variants70
NM_014516.4(CNOT3):c.732dup (p.Ser245fs)Pathogenic
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies|Inborn genetic diseases|CNOT3-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 245
NM_014516.4(CNOT3):c.2089C>T (p.Arg697Ter)Pathogenic
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies|CNOT3-associated disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 697
NM_014516.4(CNOT3):c.286C>T (p.Arg96Ter)Pathogenic
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 96
NM_014516.4(CNOT3):c.1904+2T>CPathogenic
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies
β˜…β˜…β˜†β˜†2025
NM_014516.4(CNOT3):c.1941dup (p.Tyr648fs)Pathogenic
See cases|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 648
NM_014516.4(CNOT3):c.258G>A (p.Thr86=)Likely pathogenic
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies
β˜…β˜…β˜†β˜†2024β†’ Residue 86
NM_014516.4(CNOT3):c.1979_1980del (p.Val660fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 660
NM_014516.4(CNOT3):c.821_825dup (p.Asn276fs)Pathogenic
not provided|Intellectual developmental disorder with speech delay, autism, and dysmorphic facies
β˜…β˜…β˜†β˜†2023β†’ Residue 276
NM_014516.4(CNOT3):c.241C>A (p.Arg81Ser)Likely pathogenic
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies
β˜…β˜…β˜†β˜†2022β†’ Residue 81
NM_014516.4(CNOT3):c.388-1G>CPathogenic
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies
β˜…β˜†β˜†β˜†2025
NM_014516.4(CNOT3):c.1892_1893del (p.Asp630_Ser631insTer)Pathogenic
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies
β˜…β˜†β˜†β˜†2025β†’ Residue 630
NM_014516.4(CNOT3):c.305_316del (p.Ala102_Lys105del)Likely pathogenic
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies
β˜…β˜†β˜†β˜†2025β†’ Residue 102
NM_014516.4(CNOT3):c.2081dup (p.Ser695fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 695
NM_014516.4(CNOT3):c.1189G>T (p.Gly397Ter)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2024β†’ Residue 397
NM_014516.4(CNOT3):c.119A>G (p.Gln40Arg)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 40
NM_014516.4(CNOT3):c.1708ATC[1] (p.Ile571del)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 571
NM_014516.4(CNOT3):c.766C>T (p.Gln256Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 256
NM_014516.4(CNOT3):c.1373dup (p.Ser459fs)Pathogenic
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies
β˜…β˜†β˜†β˜†2024β†’ Residue 459
NM_014516.4(CNOT3):c.22C>T (p.Gln8Ter)Pathogenic
Intellectual developmental disorder with speech delay, autism, and dysmorphic facies
β˜…β˜†β˜†β˜†2024β†’ Residue 8
NM_014516.4(CNOT3):c.2037+3A>CLikely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2023
View on ClinVar β†—
Related Genes
DDX6Protein interaction100%MMP7Protein interaction100%CNOT8Protein interaction100%CNOT4Protein interaction100%CNOT6LProtein interaction100%EXOSC1Protein interaction100%
Tissue Expression

No tissue expression data available for this gene.

Gene Interaction Network
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CNOT3DDX6MMP7CNOT8CNOT4CNOT6LEXOSC1
PROTEIN STRUCTURE
Preparing viewer…
PDB9C3H Β· 2.00 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.06Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.01 [0.00–0.06]
RankingsWhere CNOT3 stands among ~20K protein-coding genes
  • #4,109of 20,598
    Most Researched115 Β· top quartile
  • #1,041of 5,498
    Most Pathogenic Variants70 Β· top quartile
  • #11of 17,882
    Most Constrained (LOEUF)0.06 Β· top 1%
Genes detectedCNOT3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes.
PMID: 39571015
Science Β· 2024
1.00
2
T-Cell Acute Lymphoblastic Leukemia: Biomarkers and Their Clinical Usefulness.
PMID: 34440292
Genes (Basel) Β· 2021
0.90
3
Translation efficiency driven by CNOT3 subunit of the CCR4-NOT complex promotes leukemogenesis.
PMID: 38491013
Nat Commun Β· 2024
0.80
4
Specific recognition and ubiquitination of translating ribosomes by mammalian CCR4-NOT.
PMID: 37653243
Nat Struct Mol Biol Β· 2023
0.70
5
Cnot1, Cnot2, and Cnot3 maintain mouse and human ESC identity and inhibit extraembryonic differentiation.
PMID: 22367759
Stem Cells Β· 2012
0.60