CSF1R colony stimulating factor 1 receptor [Homo sapiens (human)] - Gene

Summary

Official Symbol: CSF1Rprovided by HGNC
Official Full Name: colony stimulating factor 1 receptorprovided by HGNC
Primary source: HGNC:HGNC:2433
See related: Ensembl:ENSG00000182578 MIM:164770; AllianceGenome:HGNC:2433
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: FMS; CSFR; FIM2; GPSC; HDLS; C-FMS; CD115; HDLS1; CSF-1R; BANDDOS; M-CSF-R
Summary: The protein encoded by this gene is the receptor for colony stimulating factor 1, a cytokine which controls the production, differentiation, and function of macrophages. This receptor mediates most if not all of the biological effects of this cytokine. Ligand binding activates the receptor kinase through a process of oligomerization and transphosphorylation. The encoded protein is a tyrosine kinase transmembrane receptor and member of the CSF1/PDGF receptor family of tyrosine-protein kinases. Mutations in this gene have been associated with a predisposition to myeloid malignancy. The first intron of this gene contains a transcriptionally inactive ribosomal protein L7 processed pseudogene oriented in the opposite direction. Alternative splicing results in multiple transcript variants. Expression of a splice variant from an LTR promoter has been found in Hodgkin lymphoma (HL), HL cell lines and anaplastic large cell lymphoma. [provided by RefSeq, Mar 2017]
Expression: Broad expression in spleen (RPKM 68.6), placenta (RPKM 60.0) and 22 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q32

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (150053295..150113365, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (150589842..150649957, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (149432858..149492928, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Heterozygous missense CSF1R variants hamper in vitro CD34+-derived dendritic cell generation but not in vivo dendritic cell development.
Title: Heterozygous missense CSF1R variants hamper in vitro CD34+-derived dendritic cell generation but not in vivo dendritic cell development.
Novel variants in CSF1R associated with adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP).
Title: Novel variants in CSF1R associated with adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP).
The Phenotypic and Genotypic Spectrum of CSF1R-Related Disorder in China.
Title: The Phenotypic and Genotypic Spectrum of CSF1R-Related Disorder in China.
Unifying considerations and evidence of macrophage activation mosaicism through human CSF1R and M1/M2 genes.
Title: Unifying considerations and evidence of macrophage activation mosaicism through human CSF1R and M1/M2 genes.
Colony stimulating factor-1 receptor drives glomerular parietal epithelial cell activation in focal segmental glomerulosclerosis.
Title: Colony stimulating factor-1 receptor drives glomerular parietal epithelial cell activation in focal segmental glomerulosclerosis.
An adapted protocol to derive microglia from stem cells and its application in the study of CSF1R-related disorders.
Title: An adapted protocol to derive microglia from stem cells and its application in the study of CSF1R-related disorders.
CSF1R-related disorder: State of the art, challenges, and proposition of a new terminology.
Title: CSF1R-related disorder: State of the art, challenges, and proposition of a new terminology.
A recurrent pathogenic splicing mutation of Colony-stimulating factor 1 receptor is responsible for a Chinese family with diffuse leukoencephalopathy.
Title: A recurrent pathogenic splicing mutation of Colony-stimulating factor 1 receptor is responsible for a Chinese family with diffuse leukoencephalopathy.
Inhibition of CSF1R and KIT With Pexidartinib Reduces Inflammatory Signaling and Cell Viability in Endometriosis.
Title: Inhibition of CSF1R and KIT With Pexidartinib Reduces Inflammatory Signaling and Cell Viability in Endometriosis.
Colony Stimulating Factor-1 Receptor: An emerging target for neuroinflammation PET imaging and AD therapy.
Title: Colony Stimulating Factor-1 Receptor: An emerging target for neuroinflammation PET imaging and AD therapy.

Submit: New GeneRIF Correction See all GeneRIFs (180)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Brain abnormalities, neurodegeneration, and dysosteosclerosis MedGen: C5193117 OMIM: 618476 GeneReviews: Not available	not available
Hereditary diffuse leukoencephalopathy with spheroids MedGen: C3711381 GeneReviews: CSF1R-Related Disorder	not available
Leukoencephalopathy, diffuse hereditary, with spheroids 1 MedGen: C5561929 OMIM: 221820 GeneReviews: CSF1R-Related Disorder	not available

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	HIV-1 Nef downregulates CSFR expression in M2-type macrophages	PubMed
	nef	HIV-1 Nef causes the FMS N-glycosylation defect and induces relocalization of the GM130 by activating the p56Hck/MEK/ERK/GRASP65 phosphorylation cascade in the Golgi	PubMed
	nef	HIV-1 Nef binds Hck and induces skewed Golgi-localization of Hck, which leads to Fms maturation arrest	PubMed
	nef	HIV-1 Nef inhibits the activation of M-CSF receptor signaling by means of the activation of Hck and the subsequent induction of an aberrant molecular association between Hck and M-CSF receptor complex	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH69916 (e-PCR)
- UniSTS:6912

D5S1865 (e-PCR)
- UniSTS:47366

GDB:212649 (e-PCR)
- UniSTS:156169

D5S2619 (e-PCR)
- UniSTS:54287

D5S2602 (e-PCR)
- UniSTS:56095

WI-18889 (e-PCR)
- UniSTS:44587

PMC156747P2 (e-PCR)
- UniSTS:271426

PMC156747P3 (e-PCR)
- UniSTS:271427

PMC156747P4 (e-PCR)
- UniSTS:271428

PDGFRB_1343 (e-PCR)
- UniSTS:277577

MARC_12115-12116:1004707389:1 (e-PCR)
- UniSTS:267343

GDB:192951 (e-PCR)
- UniSTS:155731

GDB:192952 (e-PCR)
- UniSTS:155732

RH15986 (e-PCR)
- UniSTS:79225

CSF1R_1770 (e-PCR)
- UniSTS:277131

D5S1469 (e-PCR), detects polymorphism
- UniSTS:81844

GDB:181638 (e-PCR)
- UniSTS:155324

WI-18300 (e-PCR)
- UniSTS:18664

D16S674 (e-PCR)
- UniSTS:24302

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables GPI-linked ephrin receptor activity	IEA Inferred from Electronic Annotation more info
enables boss receptor activity	IEA Inferred from Electronic Annotation more info
enables brain-derived neurotrophic factor receptor activity	IEA Inferred from Electronic Annotation more info
enables cytokine binding	IDA Inferred from Direct Assay more info	PubMed
enables cytokine binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables epidermal growth factor receptor activity	IEA Inferred from Electronic Annotation more info
enables fibroblast growth factor receptor activity	IEA Inferred from Electronic Annotation more info
enables growth factor binding	IBA Inferred from Biological aspect of Ancestor more info
enables hepatocyte growth factor receptor activity	IEA Inferred from Electronic Annotation more info
enables histone H2AXY142 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3Y41 kinase activity	IEA Inferred from Electronic Annotation more info
enables insulin receptor activity	IEA Inferred from Electronic Annotation more info
enables insulin-like growth factor receptor activity	IEA Inferred from Electronic Annotation more info
enables macrophage colony-stimulating factor receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables macrophage colony-stimulating factor receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables macrophage colony-stimulating factor receptor activity	ISS Inferred from Sequence or Structural Similarity more info
enables placental growth factor receptor activity	IEA Inferred from Electronic Annotation more info
enables platelet-derived growth factor alpha-receptor activity	IEA Inferred from Electronic Annotation more info
enables platelet-derived growth factor beta-receptor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables protein phosphatase binding	IEA Inferred from Electronic Annotation more info
enables protein tyrosine kinase activity	TAS Traceable Author Statement more info	PubMed
enables protein tyrosine kinase collagen receptor activity	IEA Inferred from Electronic Annotation more info
enables stem cell factor receptor activity	IEA Inferred from Electronic Annotation more info
enables transmembrane-ephrin receptor activity	IEA Inferred from Electronic Annotation more info
enables vascular endothelial growth factor receptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in Kit signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in axon guidance	IEA Inferred from Electronic Annotation more info
involved_in brain-derived neurotrophic factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell surface receptor protein tyrosine kinase signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell surface receptor protein tyrosine kinase signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell-cell junction maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to cytokine stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to macrophage colony-stimulating factor stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in collagen-activated tyrosine kinase receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in cytokine-mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ephrin receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in epidermal growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in fibroblast growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in forebrain neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in hepatocyte growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	TAS Traceable Author Statement more info	PubMed
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in insulin receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in insulin-like growth factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in macrophage colony-stimulating factor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in macrophage differentiation	TAS Traceable Author Statement more info	PubMed
involved_in mammary gland duct morphogenesis	TAS Traceable Author Statement more info	PubMed
involved_in microglial cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in monocyte differentiation	TAS Traceable Author Statement more info	PubMed
involved_in multicellular organism development	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in olfactory bulb development	IEA Inferred from Electronic Annotation more info
involved_in osteoclast differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in osteoclast differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in peptidyl-tyrosine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in platelet-derived growth factor receptor-alpha signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in platelet-derived growth factor receptor-beta signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation by host of viral process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of ERK1 and ERK2 cascade	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell motility	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of chemokine production	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of positive regulation of macrophage chemotaxis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of positive regulation of macrophage proliferation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein tyrosine kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of tyrosine phosphorylation of STAT protein	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein autophosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of MAPK cascade	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of actin cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of bone resorption	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell shape	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of macrophage migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to ischemia	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in ruffle organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction	TAS Traceable Author Statement more info	PubMed
involved_in vascular endothelial growth factor receptor-1 signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in vascular endothelial growth factor signaling pathway	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of CSF1-CSF1R complex	IBA Inferred from Biological aspect of Ancestor more info
part_of CSF1-CSF1R complex	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in cell surface	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info
located_in plasma membrane	TAS Traceable Author Statement more info
part_of receptor complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: macrophage colony-stimulating factor 1 receptor

Names: CD115 antigen; CSF-1 receptor; FMS proto-oncogene; McDonough feline sarcoma viral (v-fms) oncogene homolog; macrophage colony stimulating factor I receptor; proto-oncogene c-Fms

NP_001275634.1

EC 2.7.10.1

NP_001336665.1

EC 2.7.10.1

NP_001362249.1

EC 2.7.10.1

NP_001362250.1

EC 2.7.10.1

NP_005202.2

EC 2.7.10.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_012303.2 RefSeqGene

Range

31819..65078

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001288705.3 → NP_001275634.1 macrophage colony-stimulating factor 1 receptor isoform a precursor

See identical proteins and their annotated locations for NP_001275634.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an internal transcription initiation site compared to variant 4. Variants 1, 2, 4, and 5 all encode the same isoform (a).

Source sequence(s)

AC011382

Consensus CDS

CCDS4302.1

UniProtKB/Swiss-Prot

B5A955, D3DQG2, P07333, Q6LDW5, Q6LDY4, Q86VW7

Related

ENSP00000501699.1, ENST00000675795.1

Conserved Domains (5) summary

cd05106
Location:543 → 914

PTKc_CSF-1R; Catalytic domain of the Protein Tyrosine Kinase, Colony-Stimulating Factor-1 Receptor

smart00410
Location:28 → 85

IG_like; Immunoglobulin like

cd00096
Location:416 → 495

Ig; Immunoglobulin domain

cd04975
Location:299 → 400

Ig4_SCFR_like; Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR) and similar proteins

pfam00047
Location:207 → 293

ig; Immunoglobulin domain
NM_001349736.2 → NP_001336665.1 macrophage colony-stimulating factor 1 receptor isoform a precursor

Status: REVIEWED

Description

Transcript Variant: This variant (4) encodes the longest transcript. Variants 1, 2, 4, and 5 all encode the same isoform (a). The promoter and 5' terminal exon sequence for this variant are from a long terminal repeat (LTR). (PMID: 20436485)

Source sequence(s)

AC011382, BQ028933

Consensus CDS

CCDS4302.1

UniProtKB/Swiss-Prot

B5A955, D3DQG2, P07333, Q6LDW5, Q6LDY4, Q86VW7

Conserved Domains (5) summary

cd05106
Location:543 → 914

PTKc_CSF-1R; Catalytic domain of the Protein Tyrosine Kinase, Colony-Stimulating Factor-1 Receptor

smart00410
Location:28 → 85

IG_like; Immunoglobulin like

cd00096
Location:416 → 495

Ig; Immunoglobulin domain

cd04975
Location:299 → 400

Ig4_SCFR_like; Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR) and similar proteins

pfam00047
Location:207 → 293

ig; Immunoglobulin domain
NM_001375320.1 → NP_001362249.1 macrophage colony-stimulating factor 1 receptor isoform a precursor

Status: REVIEWED

Description

Transcript Variant: This variant (5), as well as variants 1, 2, and 4, encodes isoform a.

Source sequence(s)

AC011382

Consensus CDS

CCDS4302.1

UniProtKB/Swiss-Prot

B5A955, D3DQG2, P07333, Q6LDW5, Q6LDY4, Q86VW7

Conserved Domains (5) summary

cd05106
Location:543 → 914

PTKc_CSF-1R; Catalytic domain of the Protein Tyrosine Kinase, Colony-Stimulating Factor-1 Receptor

smart00410
Location:28 → 85

IG_like; Immunoglobulin like

cd00096
Location:416 → 495

Ig; Immunoglobulin domain

cd04975
Location:299 → 400

Ig4_SCFR_like; Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR) and similar proteins

pfam00047
Location:207 → 293

ig; Immunoglobulin domain
NM_001375321.1 → NP_001362250.1 macrophage colony-stimulating factor 1 receptor isoform b

Status: REVIEWED

Source sequence(s)

AC011382

Conserved Domains (4) summary

cd05106
Location:395 → 766

PTKc_CSF-1R; Catalytic domain of the Protein Tyrosine Kinase, Colony-Stimulating Factor-1 Receptor

smart00408
Location:69 → 137

IGc2; Immunoglobulin C-2 Type

smart00410
Location:253 → 347

IG_like; Immunoglobulin like

cd00096
Location:113 → 117

Ig; Ig strand E [structural motif]
NM_005211.4 → NP_005202.2 macrophage colony-stimulating factor 1 receptor isoform a precursor

See identical proteins and their annotated locations for NP_005202.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 4. Variants 1, 2, 4, and 5 all encode the same isoform (a).

Source sequence(s)

BC047521, BM825705, BQ028933, BX648599, X03663

Consensus CDS

CCDS4302.1

UniProtKB/Swiss-Prot

B5A955, D3DQG2, P07333, Q6LDW5, Q6LDY4, Q86VW7

Related

ENSP00000286301.3, ENST00000286301.7

Conserved Domains (5) summary

cd05106
Location:543 → 914

PTKc_CSF-1R; Catalytic domain of the Protein Tyrosine Kinase, Colony-Stimulating Factor-1 Receptor

smart00410
Location:28 → 85

IG_like; Immunoglobulin like

cd00096
Location:416 → 495

Ig; Immunoglobulin domain

cd04975
Location:299 → 400

Ig4_SCFR_like; Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR) and similar proteins

pfam00047
Location:207 → 293

ig; Immunoglobulin domain

RNA

NR_109969.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an alternate 3' exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 4, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB208819, AI863331, BM562096, CD620053, DR001419, M14193

Related

ENST00000504875.5
NR_164679.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC011382