SKIL
SKI like proto-oncogene, the group of SKI transcriptional corepressors
Basic information
Region (hg38): 3:170357342-170396835
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (81 variants)
- not_provided (2 variants)
- Prostate_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SKIL gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005414.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 78 | 83 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 78 | 4 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SKIL | protein_coding | protein_coding | ENST00000458537 | 6 | 39158 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.985 | 0.0149 | 125733 | 0 | 14 | 125747 | 0.0000557 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.928 | 296 | 344 | 0.859 | 0.0000165 | 4479 |
| Missense in Polyphen | 86 | 131.45 | 0.65426 | 1711 | ||
| Synonymous | -0.967 | 142 | 128 | 1.11 | 0.00000636 | 1267 |
| Loss of Function | 4.44 | 4 | 30.4 | 0.132 | 0.00000155 | 416 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000716 | 0.0000703 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May have regulatory role in cell division or differentiation in response to extracellular signals.;
- Pathway
- Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);TGF-Ncore;Ectoderm Differentiation;Lung fibrosis;TGF-beta Signaling Pathway;TGF-beta Receptor Signaling;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Notch;Downregulation of SMAD2/3:SMAD4 transcriptional activity;TGF-beta super family signaling pathway canonical;TGF_beta_Receptor;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;tgf beta signaling pathway;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Regulation of nuclear SMAD2/3 signaling
(Consensus)
Intolerance Scores
- loftool
- 0.0258
- rvis_EVS
- -0.33
- rvis_percentile_EVS
- 30.7
Haploinsufficiency Scores
- pHI
- 0.797
- hipred
- Y
- hipred_score
- 0.792
- ghis
- 0.537
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.997
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Skil
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); reproductive system phenotype; endocrine/exocrine gland phenotype; neoplasm; immune system phenotype; embryo phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;blastocyst formation;lymphocyte homeostasis;cell cycle arrest;transforming growth factor beta receptor signaling pathway;spermatogenesis;negative regulation of transforming growth factor beta receptor signaling pathway;negative regulation of BMP signaling pathway;response to cytokine;negative regulation of cell differentiation;neuron development;positive regulation of axonogenesis;lens fiber cell differentiation;positive regulation of extrinsic apoptotic signaling pathway via death domain receptors;positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage
- Cellular component
- acrosomal vesicle;nucleoplasm;protein-containing complex
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;chromatin binding;protein binding;SMAD binding