CSF3
colony stimulating factor 3, the group of Receptor ligands
Basic information
Region (hg38): 17:40015361-40017813
Previous symbols: [ "GCSF", "G-CSF", "C17orf33" ]
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 CSF3 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 | 10 | |||||
| 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 | 8 | 0 | 5 |
Variants in CSF3
This is a list of pathogenic ClinVar variants found in the CSF3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-40015488-C-T | not specified | Uncertain significance (Nov 14, 2023) | ||
| 17-40015500-C-T | not specified | Uncertain significance (Jun 10, 2024) | ||
| 17-40015714-A-G | not specified | Uncertain significance (Mar 27, 2023) | ||
| 17-40015720-C-T | not specified | Uncertain significance (Oct 10, 2023) | ||
| 17-40015818-C-T | Benign (Jul 06, 2018) | |||
| 17-40015825-G-A | not specified | Uncertain significance (Dec 06, 2022) | ||
| 17-40016314-A-G | not specified | Uncertain significance (Jun 29, 2022) | ||
| 17-40016509-A-G | not specified | Uncertain significance (Jun 07, 2023) | ||
| 17-40016519-T-G | not specified | Uncertain significance (Feb 27, 2024) | ||
| 17-40016578-T-G | not specified | Uncertain significance (Mar 29, 2022) | ||
| 17-40016787-C-G | Benign (Jul 10, 2018) | |||
| 17-40016804-C-A | Benign (Dec 31, 2019) | |||
| 17-40016848-G-T | Benign (Aug 20, 2018) | |||
| 17-40016854-C-T | Benign (Jul 07, 2018) | |||
| 17-40016855-G-A | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CSF3 | protein_coding | protein_coding | ENST00000225474 | 5 | 2453 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.380 | 0.610 | 125696 | 0 | 4 | 125700 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.976 | 87 | 117 | 0.746 | 0.00000667 | 1311 |
| Missense in Polyphen | 25 | 39.228 | 0.6373 | 488 | ||
| Synonymous | -0.0144 | 55 | 54.9 | 1.00 | 0.00000351 | 439 |
| Loss of Function | 2.18 | 2 | 9.11 | 0.220 | 3.91e-7 | 99 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000581 | 0.0000581 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000178 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Granulocyte/macrophage colony-stimulating factors are cytokines that act in hematopoiesis by controlling the production, differentiation, and function of 2 related white cell populations of the blood, the granulocytes and the monocytes-macrophages. This CSF induces granulocytes.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Malaria - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Hematopoietic Stem Cell Differentiation;Lung fibrosis;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Interleukin-10 signaling;PI3K-Akt Signaling Pathway;Cytokines and Inflammatory Response;Other interleukin signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Immune System;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;GPCR signaling-G alpha i
(Consensus)
Recessive Scores
- pRec
- 0.850
Intolerance Scores
- loftool
- 0.643
- rvis_EVS
- 0.22
- rvis_percentile_EVS
- 68.13
Haploinsufficiency Scores
- pHI
- 0.799
- hipred
- N
- hipred_score
- 0.203
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.817
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Csf3
- Phenotype
- hematopoietic system phenotype; renal/urinary system phenotype; immune system 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);
Zebrafish Information Network
- Gene name
- csf3b
- Affected structure
- blood island
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- immune response;multicellular organism development;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of phosphatidylinositol 3-kinase signaling;cytokine-mediated signaling pathway;positive regulation of actin filament polymerization;granulocyte differentiation;positive regulation of protein binding;positive regulation of peptidyl-serine phosphorylation;response to ethanol;positive regulation of myeloid cell differentiation;positive regulation of transcription by RNA polymerase II;positive regulation of peptidyl-tyrosine phosphorylation;positive regulation of DNA-binding transcription factor activity;positive regulation of protein kinase B signaling;cellular response to lipopolysaccharide;cellular response to cytokine stimulus;negative regulation of neuron death;positive regulation of actin cytoskeleton reorganization
- Cellular component
- extracellular region;extracellular space
- Molecular function
- cytokine activity;granulocyte colony-stimulating factor receptor binding;growth factor activity;enzyme binding