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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.
CTR9
CTR9 component of Paf1/RNA polymerase II complex
Chromosome 11 Β· 11p15.4
NCBI Gene: 9646Ensembl: ENSG00000198730.10HGNC: HGNC:16850UniProt: Q6PD62
153PubMed Papers
20Diseases
0Drugs
17Pathogenic Variants
FUNCTIONAL ROLE
Hub GeneTranscription Factor
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
negative regulation of myeloid cell differentiationtranscription elongation by RNA polymerase IICdc73/Paf1 complexstem cell population maintenanceCTR9-related neurodevelopmental disorderneurodegenerative diseasegenetic disorderhereditary Wilms tumor
✦AI Summary

CTR9 is a scaffold component of the PAF1 transcription elongation complex that associates with RNA polymerase II to regulate transcriptional elongation and histone modifications 1. The complex recruits histone-modifying enzymes, including the RNF20/40 complex for H2B ubiquitination and SET1-related complexes for H3K4me3 deposition, processes essential for transcription activation 2. CTR9 also negatively regulates PRC2-mediated H3K27me3 repressive chr11 marks, demarcating active transcriptional domains 3. Disease relevance is substantial across multiple pathologies. Loss-of-function CTR9 variants increase myeloid malignancy risk ~10-fold by expanding hematopoietic stem cells through altered super elongation complex activity 4. De novo CTR9 missense variants cause neurodevelopmental disorders with macrocephaly, motor delay, and intellectual disability through loss-of-function mechanisms 5, and CTR9 is identified among high-confidence novel neurodevelopmental disorder genes 6. Conversely, CTR9 overexpression promotes glioma progression via JAK2/STAT3 pathway activation 7, and CTR9 protein stabilization drives hepatocellular carcinoma epithelial-mesenchymal transition 8. These bidirectional roles suggest CTR9 function must be precisely balanced for normal development and cancer prevention.

Sources cited
1
CTR9 loss-of-function variants increase myeloid malignancy risk ~10-fold by expanding hematopoietic stem cells through increased super elongation complex activity
PMID: 38218188
2
CTR9 identified as high-confidence (>90% true-positive probability) candidate neurodevelopmental disorder gene through de novo variant analysis
PMID: 35468861
3
De novo CTR9 missense variants cause macrocephaly, motor delay, and intellectual disability through loss-of-normal function and dominant-negative effects
PMID: 35717577
4
CTR9 overexpression in glioma promotes proliferation, migration, and invasion through JAK2/STAT3 pathway activation
PMID: 34369006
5
CTR9 is required for normal development and histone H3K4me3 deposition; conserved PAF1 complex function across species
PMID: 27678520
6
PAF1 complex containing CTR9 displaces NELF and promotes RNA Pol II pause release during transcriptional elongation
PMID: 30135578
7
CTR9 is ubiquitinated and degraded by SIAH1, with CTR9 stabilization promoting hepatocellular carcinoma epithelial-mesenchymal transition
PMID: 37038329
8
CTR9 negatively regulates PRC2-mediated H3K27me3 repressive histone marks by controlling PRC2 subtype equilibrium
PMID: 35137163
Disease Associationsβ“˜20
CTR9-related neurodevelopmental disorderOpen Targets
0.61Moderate
neurodegenerative diseaseOpen Targets
0.52Moderate
genetic disorderOpen Targets
0.48Moderate
hereditary Wilms tumorOpen Targets
0.46Moderate
Neurodevelopmental disorderOpen Targets
0.43Moderate
Wilms tumorOpen Targets
0.42Moderate
MacrocephalyOpen Targets
0.40Weak
Motor delayOpen Targets
0.40Weak
Intellectual disabilityOpen Targets
0.37Weak
Abnormality of the cardiovascular systemOpen Targets
0.37Weak
Atypical behaviorOpen Targets
0.37Weak
Autistic behaviorOpen Targets
0.37Weak
complex neurodevelopmental disorderOpen Targets
0.37Weak
Delayed speech and language developmentOpen Targets
0.37Weak
dengue diseaseOpen Targets
0.37Weak
Failure to thriveOpen Targets
0.37Weak
Feeding difficultiesOpen Targets
0.37Weak
NephroblastomaOpen Targets
0.37Weak
alcohol drinkingOpen Targets
0.35Weak
ovarian neoplasmOpen Targets
0.28Weak
Pathogenic Variants17
NM_014633.5(CTR9):c.1364A>G (p.Asn455Ser)Likely pathogenic
CTR9-related neurodevelopmental disorder|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 455
NM_014633.5(CTR9):c.50T>C (p.Ile17Thr)Pathogenic
CTR9-related neurodevelopmental disorder|not provided|Neurodevelopmental disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 17
NM_014633.5(CTR9):c.74C>G (p.Pro25Arg)Pathogenic
CTR9-related neurodevelopmental disorder|Inborn genetic diseases
β˜…β˜…β˜†β˜†2024β†’ Residue 25
NM_014633.4(CTR9):c.1286delLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2026
NM_014633.5(CTR9):c.98T>C (p.Ile33Thr)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 33
NM_014633.5(CTR9):c.110A>G (p.Glu37Gly)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 37
NM_014633.5(CTR9):c.46-1G>TPathogenic
CTR9-related neurodevelopmental disorder
β˜…β˜†β˜†β˜†2025
NM_014633.5(CTR9):c.44A>G (p.Glu15Gly)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2024β†’ Residue 15
NM_014633.5(CTR9):c.56T>A (p.Leu19His)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2024β†’ Residue 19
NM_014633.5(CTR9):c.85G>C (p.Glu29Gln)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 29
NM_014633.5(CTR9):c.43G>A (p.Glu15Lys)Likely pathogenic
CTR9-related neurodevelopmental disorder
β˜…β˜†β˜†β˜†2021β†’ Residue 15
NM_014633.5(CTR9):c.1405G>A (p.Glu469Lys)Likely pathogenic
CTR9-related neurodevelopmental disorder
β˜…β˜†β˜†β˜†2021β†’ Residue 469
NM_014633.5(CTR9):c.254G>A (p.Cys85Tyr)Likely pathogenic
CTR9-related neurodevelopmental disorder
β˜…β˜†β˜†β˜†2021β†’ Residue 85
NM_014633.5(CTR9):c.2633G>A (p.Arg878Gln)Likely pathogenic
CTR9-related neurodevelopmental disorder
β˜…β˜†β˜†β˜†2021β†’ Residue 878
NM_014633.5(CTR9):c.109G>C (p.Glu37Gln)Likely pathogenic
CTR9-related neurodevelopmental disorder
β˜…β˜†β˜†β˜†2021β†’ Residue 37
NM_014633.5(CTR9):c.76G>C (p.Glu26Gln)Likely pathogenic
CTR9-related neurodevelopmental disorder
β˜…β˜†β˜†β˜†2021β†’ Residue 26
NM_014633.5(CTR9):c.2801A>G (p.Lys934Arg)Likely pathogenic
See cases
β˜†β˜†β˜†β˜†β†’ Residue 934
View on ClinVar β†—
Related Genes
CDK9Protein interaction100%MLLT1Protein interaction100%AFF1Protein interaction100%MLLT3Protein interaction100%PEX2Protein interaction100%ELLProtein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Heart
96%
Liver
89%
Ovary
75%
Brain
66%
Lung
62%
Gene Interaction Network
Click a node to explore
CTR9CDK9MLLT1AFF1MLLT3PEX2ELL
PROTEIN STRUCTURE
Preparing viewer…
PDB9HVQ Β· 2.00 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.37Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.28 [0.21–0.37]
RankingsWhere CTR9 stands among ~20K protein-coding genes
  • #2,949of 20,598
    Most Researched153 Β· top quartile
  • #2,326of 5,498
    Most Pathogenic Variants17
  • #1,695of 17,882
    Most Constrained (LOEUF)0.37 Β· top 10%
Genes detectedCTR9
Sources retrieved26 papers
Response timeβ€”
πŸ“„ Sources
26β–Ό
1
Inherited blood cancer predisposition through altered transcription elongation.
PMID: 38218188
Cell Β· 2024
1.00
2
Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants.
PMID: 35468861
Genome Med Β· 2022
0.90
3
Rare CTR9 variants and myeloid malignancies.
PMID: 38351318
Nat Genet Β· 2024
0.84
4
De novo non-synonymous CTR9 variants are associated with motor delay and macrocephaly: human genetic and zebrafish experimental evidence.
PMID: 35717577
Hum Mol Genet Β· 2022
0.80
5
CTR9-mediated JAK2/STAT3 pathway promotes the proliferation, migration, and invasion of human glioma cells.
PMID: 34369006
J Clin Lab Anal Β· 2021
0.70