CSF1
colony stimulating factor 1
Basic information
Region (hg38): 1:109910242-109930992
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 CSF1 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 | 20 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 20 | 3 | 3 |
Variants in CSF1
This is a list of pathogenic ClinVar variants found in the CSF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-109911030-G-A | not specified | Uncertain significance (Oct 03, 2022) | ||
| 1-109911033-C-T | not specified | Uncertain significance (Jun 16, 2023) | ||
| 1-109911058-C-G | not specified | Uncertain significance (Feb 27, 2024) | ||
| 1-109917459-A-C | not specified | Uncertain significance (Feb 02, 2022) | ||
| 1-109921853-G-C | not specified | Uncertain significance (Jan 04, 2024) | ||
| 1-109921866-A-G | not specified | Uncertain significance (Feb 15, 2023) | ||
| 1-109921915-A-C | not specified | Uncertain significance (Apr 03, 2023) | ||
| 1-109921917-C-T | not specified | Uncertain significance (Apr 09, 2024) | ||
| 1-109921985-T-G | not specified | Uncertain significance (Jun 11, 2024) | ||
| 1-109923252-C-T | not specified | Uncertain significance (Sep 27, 2021) | ||
| 1-109923354-G-C | not specified | Uncertain significance (May 09, 2023) | ||
| 1-109923364-G-A | not specified | Uncertain significance (Jan 22, 2024) | ||
| 1-109923381-C-T | not specified | Uncertain significance (Apr 06, 2024) | ||
| 1-109923397-A-G | not specified | Uncertain significance (Aug 17, 2022) | ||
| 1-109923447-G-A | not specified | Uncertain significance (May 27, 2022) | ||
| 1-109923465-C-A | not specified | Uncertain significance (Apr 12, 2022) | ||
| 1-109923478-C-A | not specified | Uncertain significance (Sep 20, 2023) | ||
| 1-109923497-G-A | Benign (Aug 05, 2018) | |||
| 1-109923580-G-T | not specified | Uncertain significance (Nov 07, 2022) | ||
| 1-109923697-C-T | not specified | Likely benign (Mar 15, 2024) | ||
| 1-109923833-G-A | Benign (Jul 16, 2018) | |||
| 1-109923855-G-A | not specified | Uncertain significance (May 15, 2024) | ||
| 1-109923910-C-T | not specified | Uncertain significance (May 31, 2023) | ||
| 1-109923913-C-T | not specified | Uncertain significance (Oct 12, 2022) | ||
| 1-109923921-G-C | not specified | Uncertain significance (Jan 30, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CSF1 | protein_coding | protein_coding | ENST00000329608 | 8 | 20751 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.996 | 0.00366 | 116733 | 0 | 1 | 116734 | 0.00000428 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.514 | 285 | 311 | 0.918 | 0.0000170 | 3592 |
| Missense in Polyphen | 79 | 104.93 | 0.7529 | 1414 | ||
| Synonymous | -0.969 | 146 | 132 | 1.11 | 0.00000788 | 1140 |
| Loss of Function | 4.04 | 1 | 21.0 | 0.0477 | 9.71e-7 | 247 |
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) | 0.00000955 | 0.00000955 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cytokine that plays an essential role in the regulation of survival, proliferation and differentiation of hematopoietic precursor cells, especially mononuclear phagocytes, such as macrophages and monocytes. Promotes the release of proinflammatory chemokines, and thereby plays an important role in innate immunity and in inflammatory processes. Plays an important role in the regulation of osteoclast proliferation and differentiation, the regulation of bone resorption, and is required for normal bone development. Required for normal male and female fertility. Promotes reorganization of the actin cytoskeleton, regulates formation of membrane ruffles, cell adhesion and cell migration. Plays a role in lipoprotein clearance. {ECO:0000269|PubMed:16337366, ECO:0000269|PubMed:19934330, ECO:0000269|PubMed:20504948, ECO:0000269|PubMed:20829061}.;
- Disease
- DISEASE: Note=Aberrant expression of CSF1 or CSF1R can promote cancer cell proliferation, invasion and formation of metastases. Overexpression of CSF1 or CSF1R is observed in a significant percentage of breast, ovarian, prostate, and endometrial cancers.; DISEASE: Note=Aberrant expression of CSF1 or CSF1R may play a role in inflammatory diseases, such as rheumatoid arthritis, glomerulonephritis, atherosclerosis, and allograft rejection.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Folate Metabolism;miR-targeted genes in muscle cell - TarBase;Differentiation Pathway;Hematopoietic Stem Cell Differentiation;Development of pulmonary dendritic cells and macrophage subsets;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Interleukin-10 signaling;PI3K-Akt Signaling Pathway;Cytokines and Inflammatory Response;Other interleukin signaling;Signaling by Interleukins;mets affect on macrophage differentiation;Post-translational protein phosphorylation;Cytokine Signaling in Immune system;Post-translational protein modification;Metabolism of proteins;Immune System;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Signaling events mediated by TCPTP;Signaling events mediated by PTP1B;Integrins in angiogenesis
(Consensus)
Recessive Scores
- pRec
- 0.607
Intolerance Scores
- loftool
- 0.0626
- rvis_EVS
- 0.29
- rvis_percentile_EVS
- 71.51
Haploinsufficiency Scores
- pHI
- 0.162
- hipred
- Y
- hipred_score
- 0.597
- ghis
- 0.470
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.955
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Csf1
- Phenotype
- vision/eye phenotype; limbs/digits/tail 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; skeleton phenotype; immune system phenotype; liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); growth/size/body region phenotype; reproductive 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); 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); craniofacial phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- positive regulation of cell-matrix adhesion;osteoclast proliferation;developmental process involved in reproduction;inflammatory response;transmembrane receptor protein tyrosine kinase signaling pathway;cell population proliferation;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of gene expression;regulation of macrophage derived foam cell differentiation;positive regulation of macrophage derived foam cell differentiation;positive regulation of macrophage chemotaxis;cytokine-mediated signaling pathway;hemopoiesis;cell differentiation;macrophage differentiation;regulation of ossification;osteoclast differentiation;positive regulation of cell migration;positive regulation of cellular protein metabolic process;positive regulation of mononuclear cell proliferation;macrophage colony-stimulating factor signaling pathway;positive regulation of multicellular organism growth;monocyte activation;positive regulation of odontogenesis of dentin-containing tooth;post-translational protein modification;cellular protein metabolic process;innate immune response;positive regulation of macrophage differentiation;positive regulation of monocyte differentiation;positive regulation of osteoclast differentiation;positive regulation of protein kinase activity;positive regulation of Ras protein signal transduction;homeostasis of number of cells within a tissue;branching involved in mammary gland duct morphogenesis;mammary gland fat development;mammary duct terminal end bud growth;positive regulation of macrophage colony-stimulating factor signaling pathway;positive regulation of microglial cell migration
- Cellular component
- extracellular region;extracellular space;endoplasmic reticulum lumen;plasma membrane;membrane;integral component of membrane;perinuclear region of cytoplasm;CSF1-CSF1R complex
- Molecular function
- cytokine activity;macrophage colony-stimulating factor receptor binding;protein binding;growth factor activity;identical protein binding;protein homodimerization activity