Seroatlas · Human Serome Atlas

CNOT9

CCR4-NOT transcription complex subunit 9

Also known as: CAF40, CNOT9_HUMAN, CT129, RCD1, RCD1+, RQCD1

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q92600
Gene
CNOT9
Ensembl
ENSG00000144580
Chromosome
2
Canonical length
299 aa
Protein class
Predicted intracellular proteins
Subcellular location
Cytoplasmic bodies
Quaternary structure
Homodimer

OverviewNCBI Gene

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 differentiation and development. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Oct 2012]

Canonical amino-acid sequenceUniProt

299 residues, UniProt reviewed canonical sequence.

>Q92600|CNOT9
     1  MHSLATAAPV PTTLAQVDRE KIYQWINELS SPETRENALL ELSKKRESVP DLAPMLWHSF
    61  GTIAALLQEI VNIYPSINPP TLTAHQSNRV CNALALLQCV ASHPETRSAF LAAHIPLFLY
   121  PFLHTVSKTR PFEYLRLTSL GVIGALVKTD EQEVINFLLT TEIIPLCLRI MESGSELSKT
   181  VATFILQKIL LDDTGLAYIC QTYERFSHVA MILGKMVLQL SKEPSARLLK HVVRCYLRLS
   241  DNPRAREALR QCLPDQLKDT TFAQVLKDDT TTKRWLAQLV KNLQEGQVTD PRGIPLPPQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CNOT9 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Intracellular
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.28
Highest tissue expression
38 nTPM

Expression across tissuesHPA

Tissue

  • bone marrow: 38 nTPM
  • tonsil: 34 nTPM
  • thymus: 31 nTPM
  • lymph node: 29 nTPM
  • testis: 25 nTPM
  • appendix: 25 nTPM

Single-cell type

  • myonuclei: 106 nCPM
  • cone photoreceptor cells: 79 nCPM
  • respiratory ciliated cells: 74 nCPM
  • erythrocyte progenitors: 72 nCPM
  • lactotrophs: 68 nCPM
  • rod photoreceptor cells: 67 nCPM

Immune cell

  • gdT-cell: 42 nTPM
  • total PBMC: 38 nTPM
  • basophil: 37 nTPM
  • MAIT T-cell: 37 nTPM
  • NK-cell: 36 nTPM
  • memory CD8 T-cell: 35 nTPM

Brain region

  • white matter: 30 nTPM
  • cerebellum: 28 nTPM
  • spinal cord: 26 nTPM
  • basal ganglia: 26 nTPM
  • hypothalamus: 25 nTPM
  • midbrain: 25 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CNOT9.

Disease | GeneticClinVar

4 pathogenic / likely-pathogenic of 34 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

  • CNOT9-associated neurodevelopmental disorder
  • See cases
  • CNOT9-related disorder

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
0.28
gnomAD pLI
0.99
DepMap mean gene effect
-0.43
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of CNOT9 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads CNOT9 as an antibody target. Whether an autoantibody or antibody against CNOT9 could matter depends on whether native CNOT9 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CNOT9 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label CNOT9 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/CNOT9. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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