SKP2
S-phase kinase associated protein 2, the group of F-box and leucine rich repeat proteins
Basic information
Region (hg38): 5:36151989-36196849
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (18 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SKP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005983.4. 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 | 0 | |||||
| missense | 18 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 18 | 0 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SKP2 | protein_coding | protein_coding | ENST00000274255 | 10 | 32331 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.960 | 0.0396 | 125742 | 0 | 6 | 125748 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.95 | 148 | 232 | 0.639 | 0.0000120 | 2753 |
| Missense in Polyphen | 21 | 54.299 | 0.38675 | 732 | ||
| Synonymous | 0.578 | 87 | 94.1 | 0.924 | 0.00000482 | 854 |
| Loss of Function | 3.90 | 3 | 23.3 | 0.129 | 0.00000127 | 250 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000119 | 0.000119 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Substrate recognition component of a SCF (SKP1-CUL1-F- box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins involved in cell cycle progression, signal transduction and transcription. Specifically recognizes phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. Degradation of CDKN1B/p27kip also requires CKS1. Recognizes target proteins ORC1, CDT1, RBL2, KMT2A/MLL1, CDK9, RAG2, FOXO1, UBP43, and probably MYC, TOB1 and TAL1. Degradation of TAL1 also requires STUB1. Recognizes CDKN1A in association with CCNE1 or CCNE2 and CDK2. Promotes ubiquitination and destruction of CDH1 in a CK1-Dependent Manner, thereby regulating cell migration. {ECO:0000269|PubMed:11931757, ECO:0000269|PubMed:12435635, ECO:0000269|PubMed:12769844, ECO:0000269|PubMed:12840033, ECO:0000269|PubMed:15342634, ECO:0000269|PubMed:15668399, ECO:0000269|PubMed:15949444, ECO:0000269|PubMed:16103164, ECO:0000269|PubMed:16262255, ECO:0000269|PubMed:16581786, ECO:0000269|PubMed:16951159, ECO:0000269|PubMed:17908926, ECO:0000269|PubMed:17962192, ECO:0000269|PubMed:22770219}.;
- Pathway
- mTOR signaling pathway - Homo sapiens (human);Cell cycle - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Ubiquitin mediated proteolysis - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Cell Cycle;Retinoblastoma (RB) in Cancer;Imatinib and Chronic Myeloid Leukemia;regulation of p27 phosphorylation during cell cycle progression;Transcriptional regulation by RUNX2;Notch;Gene expression (Transcription);e2f1 destruction pathway;Generic Transcription Pathway;Post-translational protein modification;Metabolism of proteins;RNA Polymerase II Transcription;Immune System;Cyclin D associated events in G1;G1 Phase;Adaptive Immune System;SCF(Skp2)-mediated degradation of p27/p21;Cyclin E associated events during G1/S transition ;Antigen processing: Ubiquitination & Proteasome degradation;Mitotic G1-G1/S phases;Cyclin A:Cdk2-associated events at S phase entry;Orc1 removal from chromatin;DNA Replication;Switching of origins to a post-replicative state;Class I MHC mediated antigen processing & presentation;Synthesis of DNA;S Phase;Neddylation;Ub-specific processing proteases;Deubiquitination;G1/S Transition;C-MYC pathway;Notch signaling pathway;Cell Cycle;Cell Cycle, Mitotic;FOXM1 transcription factor network;FoxO family signaling;Regulation of retinoblastoma protein;p53 pathway;Regulation of RUNX2 expression and activity
(Consensus)
Recessive Scores
- pRec
- 0.228
Intolerance Scores
- loftool
- 0.474
- rvis_EVS
- -0.69
- rvis_percentile_EVS
- 14.97
Haploinsufficiency Scores
- pHI
- 0.845
- hipred
- Y
- hipred_score
- 0.739
- ghis
- 0.684
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.818
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Skp2
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; hematopoietic system phenotype; reproductive system phenotype; liver/biliary system phenotype; renal/urinary system phenotype; immune system phenotype;
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;G2/M transition of mitotic cell cycle;protein polyubiquitination;cell population proliferation;viral process;protein deubiquitination;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;positive regulation of intracellular estrogen receptor signaling pathway;regulation of apoptotic process;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification;innate immune response;positive regulation of smooth muscle cell proliferation;defense response to virus;regulation of cell cycle;protein K48-linked ubiquitination;cellular response to cell-matrix adhesion;positive regulation of protein polyubiquitination
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytosol;SCF ubiquitin ligase complex
- Molecular function
- ubiquitin-protein transferase activity;protein binding;identical protein binding;ubiquitin protein ligase activity