CTDSPL
protein-codingCTD small phosphatase like, the group of MicroRNA protein coding host genes|CTD family phosphatases
Gene summary
Predicted to enable RNA polymerase II CTD heptapeptide repeat phosphatase activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of G1/S transition of mitotic cell cycle and negative regulation of protein phosphorylation. Located in extracellular exosome. Biomarker of lung non-small cell carcinoma. [provided by Alliance of Genome Resources, Jun 2026]
- C3orf8
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~122.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CTDSPL variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001008392.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 29 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 30 | 0 | 0 | 30 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001008393.1 | 8 | MANE Select | |
| Ensembl | ENSP00000273179.5 | 8 | MANE Select | |
| RefSeq | NP_001424957.1 | 9 | Standard | |
| RefSeq | NP_001425582.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- BMP receptor signaling
- Regulation of cytoplasmic and nuclear SMAD2/3 signaling
Biological Process
- negative regulation of protein phosphorylation
- regulation of transcription by RNA polymerase II
- protein dephosphorylation
- biological_process
- negative regulation of G1/S transition of mitotic cell cycle
Molecular Function
- molecular_function
- phosphoprotein phosphatase activity
- protein binding
- RNA polymerase II CTD heptapeptide repeat phosphatase activity
- metal ion binding
Cellular Component
- nucleus
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000273179
- Coding exons
- 8
- Length
- 122510
- Individuals with no LoFs
- 125739
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 9
- Defined
- 125748
- p
- 0.0000358
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.08 | 89 | 164 | 0.542 | 0.00000975 | 1823 |
| Missense (PolyPhen) | 14 | 57.413 | 0.24385 | 621 | ||
| Synonymous | 0.539 | 58 | 63.5 | 0.914 | 0.00000391 | 525 |
| Loss of Function | 1.67 | 6 | 12.3 | 0.487 | 5.20e-7 | 160 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000062 | rare |
| Latino/Admixed American | 0.000092 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Recruited by REST to neuronal genes that contain RE-1 elements, leading to neuronal gene silencing in non-neuronal cells (By similarity). Preferentially catalyzes the dephosphorylation of 'Ser-5' within the tandem 7 residue repeats in the C-terminal domain (CTD) of the largest RNA polymerase II subunit POLR2A. Negatively regulates RNA polymerase II transcription, possibly by controlling the transition from initiation/capping to processive transcript elongation. {ECO:0000250, ECO:0000269|PubMed:12721286}.;
Recessive Scores
- pRec
- 0.151
Intolerance Scores
- LoFtool
- 0.611
- RVIS EVS
- -0.03
- RVIS percentile EVS
- 51.4
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.658
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |