This gene is a member of the glycoprotein (gp)130 cytokine family and encodes cardiotrophin-like cytokine factor 1 (CLCF1). CLCF1 forms a heterodimer complex with cytokine receptor-like factor 1 (CRLF1). This dimer competes with ciliary neurotrophic factor (CNTF) for binding to the ciliary neurotrophic factor receptor (CNTFR) complex, and activates the Jak-STAT signaling cascad... See more...

Aliases for CLCF1 Gene

Aliases for CLCF1 Gene

  • Cardiotrophin Like Cytokine Factor 1 2 3 5
  • Novel Neurotrophin-1 2 3 4
  • BSF-3 2 3 4
  • NNT-1 2 3 4
  • BSF3 2 3 4
  • NNT1 2 3 4
  • CLC 2 3 4
  • CRLF1 Associated Cytokine-Like Factor 1 2 3
  • Cardiotrophin-Like Cytokine Factor 1 3 4
  • B-Cell-Stimulating Factor 3 3 4
  • CISS2 2 3
  • NR6 2 3
  • Neurotrophin-1/B-Cell Stimulating Factor-3 3
  • Cold-Induced Sweating Syndrome 2 2
  • B-Cell Stimulating Factor 3 2
  • B-Cell Stimulatory Factor 3 3
  • CLCF1 5

External Ids for CLCF1 Gene

Previous GeneCards Identifiers for CLCF1 Gene

  • GC11M066890
  • GC11M067131
  • GC11M063460

Summaries for CLCF1 Gene

Entrez Gene Summary for CLCF1 Gene

  • This gene is a member of the glycoprotein (gp)130 cytokine family and encodes cardiotrophin-like cytokine factor 1 (CLCF1). CLCF1 forms a heterodimer complex with cytokine receptor-like factor 1 (CRLF1). This dimer competes with ciliary neurotrophic factor (CNTF) for binding to the ciliary neurotrophic factor receptor (CNTFR) complex, and activates the Jak-STAT signaling cascade. CLCF1 can be actively secreted from cells by forming a complex with soluble type I CRLF1 or soluble CNTFR. CLCF1 is a potent neurotrophic factor, B-cell stimulatory agent and neuroendocrine modulator of pituitary corticotroph function. Defects in CLCF1 cause cold-induced sweating syndrome 2 (CISS2). This syndrome is characterized by a profuse sweating after exposure to cold as well as congenital physical abnormalities of the head and spine. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Oct 2009]

GeneCards Summary for CLCF1 Gene

CLCF1 (Cardiotrophin Like Cytokine Factor 1) is a Protein Coding gene. Diseases associated with CLCF1 include Crisponi/Cold-Induced Sweating Syndrome 2 and Cold-Induced Sweating Syndrome. Among its related pathways are PEDF Induced Signaling and Innate Immune System. Gene Ontology (GO) annotations related to this gene include protein heterodimerization activity and cytokine activity. An important paralog of this gene is CTF1.

UniProtKB/Swiss-Prot Summary for CLCF1 Gene

  • In complex with CRLF1, forms a heterodimeric neurotropic cytokine that plays a crucial role during neuronal development (Probable). Also stimulates B-cells. Binds to and activates the ILST/gp130 receptor.

Gene Wiki entry for CLCF1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CLCF1 Gene

Genomics for CLCF1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLCF1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CLCF1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CLCF1

Top Transcription factor binding sites by QIAGEN in the CLCF1 gene promoter:
  • GATA-2
  • Nkx2-5
  • Sp1
  • STAT3

Genomic Locations for CLCF1 Gene

Genomic Locations for CLCF1 Gene
chr11:67,364,168-67,374,177
(GRCh38/hg38)
Size:
10,010 bases
Orientation:
Minus strand
chr11:67,131,639-67,141,648
(GRCh37/hg19)
Size:
10,010 bases
Orientation:
Minus strand

Genomic View for CLCF1 Gene

Genes around CLCF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLCF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLCF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLCF1 Gene

Proteins for CLCF1 Gene

  • Protein details for CLCF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UBD9-CLCF1_HUMAN
    Recommended name:
    Cardiotrophin-like cytokine factor 1
    Protein Accession:
    Q9UBD9
    Secondary Accessions:
    • B4DNT4
    • Q6NZA4

    Protein attributes for CLCF1 Gene

    Size:
    225 amino acids
    Molecular mass:
    25176 Da
    Quaternary structure:
    • Forms a heteromeric complex with cardiotrophin-like cytokine CRLF1/CLF-1; the CRLF1-CLCF1 complex is a ligand for the ciliary neurotrophic factor receptor/CNTFR (PubMed:26858303). The CRLF1-CLCF1 heterodimer binds SORL1 (via N-terminal ectodomain); within this complex, the interaction is mediated predominantly by the CRLF1 moiety (PubMed:26858303). The tripartite signaling complex formed by CRLF1, CLCF1 and CNTFR also binds SORL1 (PubMed:26858303).

    Alternative splice isoforms for CLCF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLCF1 Gene

Post-translational modifications for CLCF1 Gene

  • Glycosylation at Asn29
  • Modification sites at PhosphoSitePlus

Other Protein References for CLCF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLCF1 Gene

Domains & Families for CLCF1 Gene

Gene Families for CLCF1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted secreted proteins

Protein Domains for CLCF1 Gene

Suggested Antigen Peptide Sequences for CLCF1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57490, highly similar to Cardiotrophin-like cytokine factor 1 (B4DNT4_HUMAN)
  • Novel neurotrophin-1 (CLCF1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UBD9

UniProtKB/Swiss-Prot:

CLCF1_HUMAN :
  • Belongs to the IL-6 superfamily.
Family:
  • Belongs to the IL-6 superfamily.
genes like me logo Genes that share domains with CLCF1: view

Function for CLCF1 Gene

Molecular function for CLCF1 Gene

UniProtKB/Swiss-Prot Function:
In complex with CRLF1, forms a heterodimeric neurotropic cytokine that plays a crucial role during neuronal development (Probable). Also stimulates B-cells. Binds to and activates the ILST/gp130 receptor.

Phenotypes From GWAS Catalog for CLCF1 Gene

Gene Ontology (GO) - Molecular Function for CLCF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 signaling receptor binding IPI 15272019
GO:0005125 cytokine activity IDA,NAS 10500198
GO:0005127 contributes_to ciliary neurotrophic factor receptor binding IDA 10966616
GO:0005515 protein binding IPI 10966616
GO:0008083 growth factor activity TAS 14632778
genes like me logo Genes that share ontologies with CLCF1: view
genes like me logo Genes that share phenotypes with CLCF1: view

Human Phenotype Ontology for CLCF1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CLCF1 Gene

MGI Knock Outs for CLCF1:
  • Clcf1 Clcf1<tm1Zou>
  • Clcf1 Clcf1<tm1.1(KOMP)Vlcg>

Animal Model Products

  • Taconic Biosciences Mouse Models for CLCF1

CRISPR Products

miRNA for CLCF1 Gene

miRTarBase miRNAs that target CLCF1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLCF1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CLCF1 Gene

Localization for CLCF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCF1 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLCF1 gene
Compartment Confidence
extracellular 5
mitochondrion 2
nucleus 2
plasma membrane 1
cytoskeleton 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLCF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IDA,TAS --
GO:0005615 extracellular space IEA --
GO:0097058 CRLF-CLCF1 complex IBA,IDA 10966616
GO:0097059 CNTFR-CLCF1 complex IBA,IDA 11285233
genes like me logo Genes that share ontologies with CLCF1: view

Pathways & Interactions for CLCF1 Gene

genes like me logo Genes that share pathways with CLCF1: view

Pathways by source for CLCF1 Gene

1 GeneGo (Thomson Reuters) pathway for CLCF1 Gene
  • Development CNTF receptor signaling

SIGNOR curated interactions for CLCF1 Gene

Activates:

Gene Ontology (GO) - Biological Process for CLCF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002639 positive regulation of immunoglobulin production ISS --
GO:0007166 cell surface receptor signaling pathway ISS --
GO:0007259 JAK-STAT cascade ISS --
GO:0008284 positive regulation of cell proliferation IDA 10966616
GO:0019221 cytokine-mediated signaling pathway NAS,TAS --
genes like me logo Genes that share ontologies with CLCF1: view

Drugs & Compounds for CLCF1 Gene

(1) Drugs for CLCF1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for CLCF1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CLCF1: view

Transcripts for CLCF1 Gene

mRNA/cDNA for CLCF1 Gene

2 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CLCF1

Alternative Splicing Database (ASD) splice patterns (SP) for CLCF1 Gene

No ASD Table

Relevant External Links for CLCF1 Gene

GeneLoc Exon Structure for
CLCF1

Expression for CLCF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CLCF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CLCF1 Gene

This gene is overexpressed in Monocytes (19.4), Urine (15.9), and Tlymphocyte (13.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CLCF1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CLCF1

SOURCE GeneReport for Unigene cluster for CLCF1 Gene:

Hs.502977

mRNA Expression by UniProt/SwissProt for CLCF1 Gene:

Q9UBD9-CLCF1_HUMAN
Tissue specificity: Expressed predominantly in lymph nodes, spleen, peripheral blood lymphocytes, bone marrow, and fetal liver.

Evidence on tissue expression from TISSUES for CLCF1 Gene

  • Kidney(4.4)
  • Lung(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CLCF1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • skull
  • tooth
  • vocal cord
Thorax:
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shoulder
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • sweat gland
  • vertebrae
genes like me logo Genes that share expression patterns with CLCF1: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for CLCF1 Gene

Orthologs for CLCF1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLCF1 Gene

Organism Taxonomy Gene Similarity Type Details
Dog
(Canis familiaris)
Mammalia CLCF1 30 31
  • 92.74 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Clcf1 30 17 31
  • 91.7 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Clcf1 30
  • 89.54 (n)
Cow
(Bos Taurus)
Mammalia CLCF1 30 31
  • 87.19 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CLCF1 31
  • 79 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CLCF1 31
  • 31 (a)
OneToOne
Chimpanzee
(Pan troglodytes)
Mammalia CTF2 31
  • 29 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CLCF1 30 31
  • 74.16 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CLCF1 31
  • 63 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia clcf1 30
  • 60.9 (n)
Str.16134 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.32246 30
Zebrafish
(Danio rerio)
Actinopterygii LOC562247 30
  • 54.74 (n)
clcf1 31
  • 24 (a)
OneToOne
Species where no ortholog for CLCF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CLCF1 Gene

ENSEMBL:
Gene Tree for CLCF1 (if available)
TreeFam:
Gene Tree for CLCF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CLCF1: view image

Paralogs for CLCF1 Gene

Paralogs for CLCF1 Gene

genes like me logo Genes that share paralogs with CLCF1: view

Variants for CLCF1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CLCF1 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
712600 Likely Benign: not provided 67,367,555(-) G/A MISSENSE_VARIANT
713415 Benign: not provided 67,365,147(-) GAGCCCCC/G FRAMESHIFT_VARIANT
730799 Likely Benign: not provided 67,367,619(-) C/T SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT
738649 Likely Benign: not provided 67,365,535(-) C/T SYNONYMOUS_VARIANT
764718 Likely Benign: not provided 67,365,427(-) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for CLCF1 Gene

Structural Variations from Database of Genomic Variants (DGV) for CLCF1 Gene

Variant ID Type Subtype PubMed ID
dgv52n111 CNV deletion 26073780
esv3361899 CNV duplication 20981092
nsv1070466 CNV deletion 25765185
nsv468603 CNV loss 19166990
nsv555253 CNV loss 21841781
nsv7220 OTHER inversion 18451855

Variation tolerance for CLCF1 Gene

Residual Variation Intolerance Score: 57.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.61; 45.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLCF1 Gene

Human Gene Mutation Database (HGMD)
CLCF1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLCF1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLCF1 Gene

Disorders for CLCF1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for CLCF1 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CLCF1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CLCF1_HUMAN
  • Crisponi/Cold-induced sweating syndrome 2 (CISS2) [MIM:610313]: An autosomal recessive disorder characterized by profuse sweating induced by cool surroundings (temperatures of 7 to 18 degrees Celsius). Patients manifest, in the neonatal period, orofacial weakness with impaired sucking and swallowing, resulting in poor feeding. Affected infants show a tendency to startle, with contractions of the facial muscles in response to tactile stimuli or during crying, trismus, abundant salivation, and opisthotonus. These features are referred to as Crisponi syndrome and can result in early death in infancy. Patients who survive into childhood have hyperhidrosis, mainly of the upper body, in response to cold temperatures, and sweat very little with heat. Additional abnormalities include a high-arched palate, nasal voice, depressed nasal bridge, inability to fully extend the elbows and kyphoscoliosis. {ECO:0000269 PubMed:16782820}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with CLCF1: view

No data available for Genatlas for CLCF1 Gene

Publications for CLCF1 Gene

  1. Inactivation of cardiotrophin-like cytokine, a second ligand for ciliary neurotrophic factor receptor, leads to cold-induced sweating syndrome in a patient. (PMID: 16782820) Rousseau F … Boman H (Proceedings of the National Academy of Sciences of the United States of America 2006) 2 3 4 23
  2. Computational EST database analysis identifies a novel member of the neuropoietic cytokine family. (PMID: 10448081) Shi Y … Alderson RF (Biochemical and biophysical research communications 1999) 2 3 4 23
  3. Novel neurotrophin-1/B cell-stimulating factor-3: a cytokine of the IL-6 family. (PMID: 10500198) Senaldi G … Chang MS (Proceedings of the National Academy of Sciences of the United States of America 1999) 2 3 4
  4. Cytokine-Like Factor 1, an Essential Facilitator of Cardiotrophin-Like Cytokine:Ciliary Neurotrophic Factor Receptor α Signaling and sorLA-Mediated Turnover. (PMID: 26858303) Larsen JV … Petersen CM (Molecular and cellular biology 2016) 3 4
  5. Ciliary neurotrophic factor, cardiotrophin-like cytokine, and neuropoietin share a conserved binding site on the ciliary neurotrophic factor receptor alpha chain. (PMID: 18728012) Rousseau F … Gascan H (The Journal of biological chemistry 2008) 3 23

Products for CLCF1 Gene

Sources for CLCF1 Gene