CTR9
CTR9 homolog, Paf1/RNA polymerase II complex component
Gene Information Card
| Symbol | CTR9 |
|---|---|
| Full Name | CTR9 homolog, Paf1/RNA polymerase II complex component |
| Gene Type | protein-coding |
| Chromosomal Location | 11p15.4 |
| NCBI Gene ID | 9646 ncbi.nlm.nih.gov/gene/9646 |
| Ensembl ID | ENSG00000149311 |
| UniProt ID | Q6PD62 |
| OMIM ID | 616714 |
| HGNC ID | 16850 |
| Aliases | hCTR9, SH2BP1, Paf1c subunit |
Description
CTR9 is a core component of the Paf1 complex (PAF1C), which associates with RNA polymerase II and regulates transcriptional elongation, chromatin modification, and mRNA processing. It is involved in the regulation of gene expression, cell cycle progression, and development. Mutations in CTR9 have been linked to Wilms tumor and neurodevelopmental disorders.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Wilms tumor (nephroblastoma) | Loss-of-function mutations in CTR9 disrupt Paf1 complex function, leading to aberrant transcriptional regulation and tumorigenesis. | PMID: 25670082, PMID: 28481328 |
| Intellectual disability | Homozygous and compound heterozygous CTR9 mutations impair neuronal gene expression, causing neurodevelopmental phenotypes. | PMID: 28481328 |
| Autism spectrum disorder | Rare CTR9 variants identified in ASD cohorts suggest contribution to synaptic gene dysregulation. | PMID: 28481328 |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 38.2 | High |
| Bone marrow | 25.1 | Medium |
| Lymph node | 22.8 | Medium |
| Brain (cerebellum) | 18.5 | Medium |
| Heart | 15.3 | Medium |
| Liver | 12.0 | Low |
| Pancreas | 10.5 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| K562 (leukemia) | 35.4 | High expression |
| HeLa (cervical) | 28.7 | High expression |
| HepG2 (liver) | 20.1 | Medium expression |
| A549 (lung) | 18.9 | Medium expression |
| SH-SY5Y (neuroblastoma) | 22.3 | Medium expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.166C>T (p.Arg56*) | Nonsense | Rare | Loss of function; truncation of CTR9 protein |
| c.1042C>T (p.Arg348*) | Nonsense | Rare | Loss of function; premature stop codon |
| c.2023_2024del (p.Leu675Glufs*3) | Frameshift | Rare | Loss of function; protein truncation |
| c.2545G>A (p.Gly849Arg) | Missense | Rare | Likely damaging; disrupts Paf1 complex interaction |
Mutation functional classification
Loss of Function (LOF)
Nonsense and frameshift mutations in CTR9 lead to truncated or absent protein, impairing Paf1 complex assembly and transcriptional regulation.
Gain of Function (GOF)
No gain-of-function mutations have been reported for CTR9.
Dominant Negative (DN)
No dominant-negative mutations have been characterized for CTR9.
View complete mutation data：
Gene Ontology (GO)
Pathways
• PAF1 complex (Reactome: R-HSA-5250941)
• RNA polymerase II transcription elongation (Reactome: R-HSA-75955)
• Chromatin modifying enzymes (Reactome: R-HSA-3247509)
Protein Summary
CTR9 is a 1173-amino acid protein that serves as a scaffold within the Paf1 complex. It interacts with other Paf1 complex subunits (e.g., PAF1, LEO1, CDC73) and with RNA polymerase II to facilitate transcriptional elongation and histone modification. The protein contains multiple tetratricopeptide repeat (TPR) domains that mediate protein-protein interactions. CTR9 is ubiquitously expressed, with highest levels in testis and bone marrow.
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