CSK
C-terminal Src kinase, the group of SH2 domain containing|Csk family tyrosine kinases
Basic information
Region (hg38): 15:74782080-74803197
Links
Phenotypes
GenCC
Source:
No genCC data.
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 CSK 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 | |||||
| missense | 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 | 8 | 1 | 2 |
Variants in CSK
This is a list of pathogenic ClinVar variants found in the CSK region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-74798663-G-A | not specified | Uncertain significance (Jan 19, 2024) | ||
| 15-74798720-G-A | not specified | Uncertain significance (Jul 16, 2024) | ||
| 15-74798834-C-G | not specified | Uncertain significance (Feb 13, 2024) | ||
| 15-74798863-G-A | not specified | Uncertain significance (May 12, 2024) | ||
| 15-74798889-G-A | not specified | Uncertain significance (Jan 24, 2024) | ||
| 15-74799293-A-C | Likely benign (Oct 01, 2022) | |||
| 15-74799310-G-A | not specified | Uncertain significance (Jan 02, 2024) | ||
| 15-74799319-A-G | not specified | Likely benign (Nov 13, 2024) | ||
| 15-74799325-C-T | not specified | Uncertain significance (Jun 07, 2023) | ||
| 15-74799396-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
| 15-74800853-A-G | not specified | Uncertain significance (Aug 20, 2024) | ||
| 15-74800861-G-A | not specified | Uncertain significance (Nov 24, 2024) | ||
| 15-74801568-G-A | Benign (Jun 12, 2018) | |||
| 15-74801841-C-T | not specified | Uncertain significance (Dec 13, 2022) | ||
| 15-74802368-A-G | not specified | Uncertain significance (Jun 11, 2021) | ||
| 15-74802379-G-A | not specified | Uncertain significance (Aug 01, 2024) | ||
| 15-74802388-G-A | not specified | Uncertain significance (Aug 01, 2024) | ||
| 15-74802442-G-A | Benign (Feb 01, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CSK | protein_coding | protein_coding | ENST00000220003 | 12 | 21142 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000234 | 124652 | 0 | 1 | 124653 | 0.00000401 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.98 | 103 | 295 | 0.349 | 0.0000193 | 2914 |
| Missense in Polyphen | 34 | 156.76 | 0.2169 | 1542 | ||
| Synonymous | 0.168 | 124 | 126 | 0.981 | 0.00000917 | 877 |
| Loss of Function | 4.76 | 1 | 28.3 | 0.0353 | 0.00000163 | 293 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000164 |
dbNSFP
Source:
- Function
- FUNCTION: Non-receptor tyrosine-protein kinase that plays an important role in the regulation of cell growth, differentiation, migration and immune response. Phosphorylates tyrosine residues located in the C-terminal tails of Src-family kinases (SFKs) including LCK, SRC, HCK, FYN, LYN, CSK or YES1. Upon tail phosphorylation, Src-family members engage in intramolecular interactions between the phosphotyrosine tail and the SH2 domain that result in an inactive conformation. To inhibit SFKs, CSK is recruited to the plasma membrane via binding to transmembrane proteins or adapter proteins located near the plasma membrane. Suppresses signaling by various surface receptors, including T- cell receptor (TCR) and B-cell receptor (BCR) by phosphorylating and maintaining inactive several positive effectors such as FYN or LCK. {ECO:0000269|PubMed:1639064, ECO:0000269|PubMed:9281320}.;
- Pathway
- Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);VEGF Signaling Pathway;Integrin-mediated Cell Adhesion;Integrated Lung Cancer Pathway;VEGFA-VEGFR2 Signaling Pathway;Chemokine signaling pathway;EGF-EGFR Signaling Pathway;Regulation of Actin Cytoskeleton;MAP2K and MAPK activation;Disease;Signal Transduction;erk and pi-3 kinase are necessary for collagen binding in corneal epithelia;integrin signaling pathway;vegf hypoxia and angiogenesis;activation of csk by camp-dependent protein kinase inhibits signaling through the t cell receptor;Phosphorylation of CD3 and TCR zeta chains;TCR signaling;PD-1 signaling;Costimulation by the CD28 family;Integrin alphaIIb beta3 signaling;Immune System;Adaptive Immune System;Signaling by EGFR;Platelet Aggregation (Plug Formation);cell to cell adhesion signaling;Platelet activation, signaling and aggregation;IL-7 signaling;EGFR1;Integrin signaling;CXCR4-mediated signaling events;Hemostasis;GAB1 signalosome;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;BCR signaling pathway;JAK STAT pathway and regulation;EPO signaling;Signaling by Receptor Tyrosine Kinases;Signaling by RAS mutants;VEGF;Signaling by high-kinase activity BRAF mutants;Signaling by moderate kinase activity BRAF mutants;Paradoxical activation of RAF signaling by kinase inactive BRAF;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction;TCR signaling in naïve CD8+ T cells;PDGFR-beta signaling pathway;Signaling events mediated by PTP1B;TCR signaling in naïve CD4+ T cells
(Consensus)
Recessive Scores
- pRec
- 0.671
Intolerance Scores
- loftool
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 43.57
Haploinsufficiency Scores
- pHI
- 0.691
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.477
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.989
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Csk
- Phenotype
- respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); normal phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; immune system phenotype; cellular phenotype; taste/olfaction phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- csk
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- decreased length
Gene ontology
- Biological process
- adaptive immune response;protein phosphorylation;brain development;negative regulation of cell population proliferation;negative regulation of low-density lipoprotein particle clearance;peptidyl-tyrosine phosphorylation;T cell costimulation;negative regulation of interleukin-6 production;negative regulation of kinase activity;adherens junction organization;negative regulation of Golgi to plasma membrane protein transport;positive regulation of MAP kinase activity;negative regulation of bone resorption;protein autophosphorylation;oligodendrocyte differentiation;negative regulation of phagocytosis;T cell receptor signaling pathway;regulation of Fc receptor mediated stimulatory signaling pathway;negative regulation of ERK1 and ERK2 cascade;cellular response to peptide hormone stimulus
- Cellular component
- cytoplasm;cytosol;plasma membrane;cell-cell junction;membrane raft;extracellular exosome
- Molecular function
- protein tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;protein binding;ATP binding;protein C-terminus binding;kinase activity;protein phosphatase binding;protein kinase A catalytic subunit binding;identical protein binding;metal ion binding;proline-rich region binding