CSF2
colony stimulating factor 2
Basic information
Region (hg38): 5:132073789-132076170
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 CSF2 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 | 3 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 3 | 3 |
Variants in CSF2
This is a list of pathogenic ClinVar variants found in the CSF2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-132073881-G-A | not specified | Likely benign (Dec 15, 2022) | ||
| 5-132073884-C-T | not specified | Uncertain significance (Mar 07, 2024) | ||
| 5-132073888-C-T | not specified | Likely benign (Dec 07, 2021) | ||
| 5-132073889-G-A | Benign (Aug 29, 2018) | |||
| 5-132073904-G-A | Benign (Jul 23, 2018) | |||
| 5-132073979-G-C | not specified | Uncertain significance (Nov 10, 2024) | ||
| 5-132074859-G-C | not specified | Uncertain significance (Oct 10, 2023) | ||
| 5-132074884-C-T | Benign (Jul 06, 2018) | |||
| 5-132074924-C-A | not specified | Uncertain significance (Dec 09, 2023) | ||
| 5-132074934-C-T | not specified | Likely benign (Aug 20, 2024) | ||
| 5-132074935-G-A | Likely benign (Jun 27, 2018) | |||
| 5-132075761-C-T | Likely benign (Jul 26, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CSF2 | protein_coding | protein_coding | ENST00000296871 | 4 | 2377 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.835 | 0.162 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.377 | 70 | 79.4 | 0.881 | 0.00000489 | 932 |
| Missense in Polyphen | 17 | 23.685 | 0.71776 | 319 | ||
| Synonymous | 0.317 | 28 | 30.2 | 0.927 | 0.00000151 | 282 |
| Loss of Function | 2.26 | 0 | 5.93 | 0.00 | 2.60e-7 | 66 |
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 | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cytokine that stimulates the growth and differentiation of hematopoietic precursor cells from various lineages, including granulocytes, macrophages, eosinophils and erythrocytes. {ECO:0000269|PubMed:3925454}.;
- Pathway
- T cell receptor signaling pathway - Homo sapiens (human);Fc epsilon RI signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Salmonella infection - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Acute myeloid leukemia - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Fc Epsilon Receptor I Signaling in Mast Cells;JAK-STAT-Core;Hematopoietic Stem Cell Differentiation;Photodynamic therapy-induced NF-kB survival signaling;Lung fibrosis;T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection;Development of pulmonary dendritic cells and macrophage subsets;Interleukin-10 signaling;Transcriptional regulation by RUNX1;Cytokines and Inflammatory Response;Signaling by GPCR;Signal Transduction;Gene expression (Transcription);Signaling by Interleukins;Generic Transcription Pathway;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;RNA Polymerase II Transcription;Immune System;Interleukin receptor SHC signaling;Interleukin-2 family signaling;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;Glucocorticoid receptor regulatory network;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;JAK STAT pathway and regulation;GPCR signaling-G alpha i;RUNX1 regulates transcription of genes involved in differentiation of myeloid cells;G beta:gamma signalling through PI3Kgamma;G-protein beta:gamma signalling;GPCR downstream signalling;Transcriptional regulation by RUNX1;GMCSF-mediated signaling events;Alpha9 beta1 integrin signaling events;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;AP-1 transcription factor network;Regulation of retinoblastoma protein;Calcium signaling in the CD4+ TCR pathway;Syndecan-2-mediated signaling events;Interleukin-3, 5 and GM-CSF signaling
(Consensus)
Recessive Scores
- pRec
- 0.812
Intolerance Scores
- loftool
- rvis_EVS
- 0.41
- rvis_percentile_EVS
- 76.67
Haploinsufficiency Scores
- pHI
- 0.925
- hipred
- N
- hipred_score
- 0.303
- ghis
- 0.419
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.826
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Csf2
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland 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); embryo phenotype; renal/urinary system phenotype; skeleton phenotype; immune system 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); neoplasm; 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); 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); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype;
Gene ontology
- Biological process
- MAPK cascade;histamine secretion;embryonic placenta development;immune response;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of gene expression;positive regulation of macrophage derived foam cell differentiation;peptidyl-tyrosine phosphorylation;cytokine-mediated signaling pathway;neutrophil differentiation;monocyte differentiation;positive regulation of interleukin-23 production;response to silicon dioxide;response to fluid shear stress;epithelial fluid transport;macrophage activation;positive regulation of tyrosine phosphorylation of STAT protein;myeloid dendritic cell differentiation;regulation of circadian sleep/wake cycle, sleep;regulation of myeloid cell differentiation;negative regulation of transcription, DNA-templated;negative regulation of cytolysis;cellular response to lipopolysaccharide;positive regulation of podosome assembly;cellular response to granulocyte macrophage colony-stimulating factor stimulus;dendritic cell differentiation;negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
- Cellular component
- extracellular region;extracellular space;intracellular membrane-bounded organelle
- Molecular function
- protein tyrosine kinase activity;Ras guanyl-nucleotide exchange factor activity;cytokine activity;granulocyte macrophage colony-stimulating factor receptor binding;protein binding;growth factor activity