SKIL

SKI like proto-oncogene, the group of SKI transcriptional corepressors

Basic information

Region (hg38): 3:170357342-170396835

Links

ENSG00000136603 ∙ NCBI:6498 ∙ OMIM:165340 ∙ HGNC:10897 ∙ Uniprot:P12757 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SKIL gene.

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.

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					1	1
missense			32	4	1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	4	2

Variants in SKIL

This is a list of pathogenic ClinVar variants found in the SKIL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-170360372-C-T		not specified	Uncertain significance (Jan 23, 2023)
3-170360392-A-G		not specified	Uncertain significance (Jan 26, 2023)
3-170360401-G-C		not specified	Uncertain significance (May 08, 2023)
3-170360530-G-C		not specified	Uncertain significance (Dec 19, 2023)
3-170360675-G-T		not specified	Uncertain significance (Apr 20, 2023)
3-170360773-G-A		not specified	Uncertain significance (Jan 09, 2024)
3-170360825-T-A		not specified	Uncertain significance (Jun 22, 2023)
3-170360905-A-T		not specified	Uncertain significance (May 25, 2022)
3-170360924-C-G		not specified	Uncertain significance (Feb 14, 2023)
3-170361035-G-A		not specified	Uncertain significance (Aug 08, 2023)
3-170361039-A-G			Benign (Jun 27, 2018)
3-170361071-C-T		not specified	Uncertain significance (Sep 14, 2022)
3-170361104-C-G		not specified	Uncertain significance (Jul 12, 2022)
3-170361179-A-G		not specified	Uncertain significance (Mar 29, 2023)
3-170361273-A-T		Malignant tumor of prostate	Uncertain significance (-)
3-170361413-A-C		not specified	Uncertain significance (Feb 13, 2024)
3-170361416-G-A		not specified	Uncertain significance (Apr 21, 2022)
3-170381275-C-T		not specified	Uncertain significance (Dec 21, 2022)
3-170381289-A-G		not specified	Uncertain significance (Sep 26, 2023)
3-170384543-T-C		not specified	Uncertain significance (Dec 28, 2022)
3-170384636-A-T		not specified	Uncertain significance (May 29, 2024)
3-170384646-A-T		not specified	Uncertain significance (Jul 20, 2021)
3-170384705-T-C		not specified	Uncertain significance (Dec 04, 2023)
3-170384708-C-T		not specified	Uncertain significance (Sep 26, 2023)
3-170384760-G-A		not specified	Likely benign (Jan 31, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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