CSF1

colony stimulating factor 1

Basic information

Region (hg38): 1:109910241-109930992

Links

ENSG00000184371 ∙ NCBI:1435 ∙ OMIM:120420 ∙ HGNC:2432 ∙ Uniprot:P09603 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSF1 gene.

• Inborn genetic diseases (13 variants)
• not provided (4 variants)

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	3
missense			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	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)
1-109923252-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)
1-109923397-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)
1-109923833-G-A			Benign (Jul 16, 2018)
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)
1-109923966-C-T		not specified	Uncertain significance (Apr 22, 2022)
1-109924063-A-T		not specified	Uncertain significance (Dec 27, 2023)
1-109924105-A-G		not specified	Likely benign (Oct 02, 2023)
1-109924154-C-T			Benign (Aug 16, 2018)
1-109924783-A-G		not specified	Likely benign (Sep 30, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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