CTDSPL
Basic information
Region (hg38): 3:37861880-37984469
Previous symbols: [ "C3orf8" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTDSPL gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in CTDSPL
This is a list of pathogenic ClinVar variants found in the CTDSPL region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CTDSPL | protein_coding | protein_coding | ENST00000273179 | 8 | 122510 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00267 | 0.941 | 125739 | 0 | 9 | 125748 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.08 | 89 | 164 | 0.542 | 0.00000975 | 1823 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000156 | 0.000153 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000113 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000179 | 0.0000176 |
| Middle Eastern | 0.000113 | 0.000109 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- BMP receptor signaling;Regulation of cytoplasmic and nuclear SMAD2/3 signaling
(Consensus)
Recessive Scores
- pRec
- 0.151
Intolerance Scores
- loftool
- 0.611
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.240
- hipred
- N
- hipred_score
- 0.446
- ghis
- 0.549
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.658
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ctdspl
- Phenotype
- homeostasis/metabolism phenotype; skeleton phenotype; limbs/digits/tail phenotype;
Gene ontology
- 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
- Cellular component
- nucleus;extracellular exosome
- Molecular function
- molecular_function;phosphoprotein phosphatase activity;protein binding;RNA polymerase II CTD heptapeptide repeat phosphatase activity;metal ion binding